diff --git a/.gitattributes b/.gitattributes index bc543944..73fdf957 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,3 +1,4 @@ # Apply override to all files in the directory (source: https://github.com/github/linguist/blob/master/docs/overrides.md) data/** linguist-vendored transformato/toppar/** linguist-vendored +transformato/_version.py export-subst diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index c853ff8e..60a57b4f 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -6,12 +6,10 @@ on: # Both are tracked here to keep legacy and new codes working push: branches: - - "master" - - "main" + - '**' pull_request: branches: - - "master" - - "main" + - '**' schedule: # Nightly tests run on master by default: # Scheduled workflows run on the latest commit on the default or base branch. diff --git a/devtools/conda-envs/fep_env.yaml b/devtools/conda-envs/fep_env.yaml index 95cb024d..98069b1f 100644 --- a/devtools/conda-envs/fep_env.yaml +++ b/devtools/conda-envs/fep_env.yaml @@ -8,7 +8,7 @@ dependencies: - openmmtools - numpy - ipython - - pymbar + - pymbar=3 - rdkit - parmed - pyyaml diff --git a/transformato/.vscode/settings.json b/transformato/.vscode/settings.json new file mode 100644 index 00000000..3e99ede3 --- /dev/null +++ b/transformato/.vscode/settings.json @@ -0,0 +1,7 @@ +{ + "python.testing.pytestArgs": [ + "." + ], + "python.testing.unittestEnabled": false, + "python.testing.pytestEnabled": true +} \ No newline at end of file diff --git a/transformato/_version.py b/transformato/_version.py index 04cda69e..be21b81a 100644 --- a/transformato/_version.py +++ b/transformato/_version.py @@ -5,8 +5,9 @@ # directories (produced by setup.py build) will contain a much shorter file # that just contains the computed version number. -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) +# This file is released into the public domain. +# Generated by versioneer-0.29 +# https://github.com/python-versioneer/python-versioneer """Git implementation of _version.py.""" @@ -15,9 +16,11 @@ import re import subprocess import sys +from typing import Any, Callable, Dict, List, Optional, Tuple +import functools -def get_keywords(): +def get_keywords() -> Dict[str, str]: """Get the keywords needed to look up the version information.""" # these strings will be replaced by git during git-archive. # setup.py/versioneer.py will grep for the variable names, so they must @@ -33,8 +36,15 @@ def get_keywords(): class VersioneerConfig: """Container for Versioneer configuration parameters.""" + VCS: str + style: str + tag_prefix: str + parentdir_prefix: str + versionfile_source: str + verbose: bool -def get_config(): + +def get_config() -> VersioneerConfig: """Create, populate and return the VersioneerConfig() object.""" # these strings are filled in when 'setup.py versioneer' creates # _version.py @@ -52,13 +62,13 @@ class NotThisMethod(Exception): """Exception raised if a method is not valid for the current scenario.""" -LONG_VERSION_PY = {} -HANDLERS = {} +LONG_VERSION_PY: Dict[str, str] = {} +HANDLERS: Dict[str, Dict[str, Callable]] = {} -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): +def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator + """Create decorator to mark a method as the handler of a VCS.""" + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} @@ -67,22 +77,35 @@ def decorate(f): return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): +def run_command( + commands: List[str], + args: List[str], + cwd: Optional[str] = None, + verbose: bool = False, + hide_stderr: bool = False, + env: Optional[Dict[str, str]] = None, +) -> Tuple[Optional[str], Optional[int]]: """Call the given command(s).""" assert isinstance(commands, list) - p = None - for c in commands: + process = None + + popen_kwargs: Dict[str, Any] = {} + if sys.platform == "win32": + # This hides the console window if pythonw.exe is used + startupinfo = subprocess.STARTUPINFO() + startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW + popen_kwargs["startupinfo"] = startupinfo + + for command in commands: try: - dispcmd = str([c] + args) + dispcmd = str([command] + args) # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) + process = subprocess.Popen([command] + args, cwd=cwd, env=env, + stdout=subprocess.PIPE, + stderr=(subprocess.PIPE if hide_stderr + else None), **popen_kwargs) break - except EnvironmentError: - e = sys.exc_info()[1] + except OSError as e: if e.errno == errno.ENOENT: continue if verbose: @@ -93,18 +116,20 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, if verbose: print("unable to find command, tried %s" % (commands,)) return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: + stdout = process.communicate()[0].strip().decode() + if process.returncode != 0: if verbose: print("unable to run %s (error)" % dispcmd) print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode + return None, process.returncode + return stdout, process.returncode -def versions_from_parentdir(parentdir_prefix, root, verbose): +def versions_from_parentdir( + parentdir_prefix: str, + root: str, + verbose: bool, +) -> Dict[str, Any]: """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both @@ -113,15 +138,14 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): """ rootdirs = [] - for i in range(3): + for _ in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return {"version": dirname[len(parentdir_prefix):], "full-revisionid": None, "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level + rootdirs.append(root) + root = os.path.dirname(root) # up a level if verbose: print("Tried directories %s but none started with prefix %s" % @@ -130,41 +154,48 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): @register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): +def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. - keywords = {} + keywords: Dict[str, str] = {} try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: + with open(versionfile_abs, "r") as fobj: + for line in fobj: + if line.strip().startswith("git_refnames ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["refnames"] = mo.group(1) + if line.strip().startswith("git_full ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["full"] = mo.group(1) + if line.strip().startswith("git_date ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["date"] = mo.group(1) + except OSError: pass return keywords @register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): +def git_versions_from_keywords( + keywords: Dict[str, str], + tag_prefix: str, + verbose: bool, +) -> Dict[str, Any]: """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") + if "refnames" not in keywords: + raise NotThisMethod("Short version file found") date = keywords.get("date") if date is not None: + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] + # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 # -like" string, which we must then edit to make compliant), because @@ -177,11 +208,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) + refs = {r.strip() for r in refnames.strip("()").split(",")} # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) + tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -190,7 +221,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) + tags = {r for r in refs if re.search(r'\d', r)} if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -199,6 +230,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): r = ref[len(tag_prefix):] + # Filter out refs that exactly match prefix or that don't start + # with a number once the prefix is stripped (mostly a concern + # when prefix is '') + if not re.match(r'\d', r): + continue if verbose: print("picking %s" % r) return {"version": r, @@ -214,7 +250,12 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): @register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): +def git_pieces_from_vcs( + tag_prefix: str, + root: str, + verbose: bool, + runner: Callable = run_command +) -> Dict[str, Any]: """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* @@ -225,8 +266,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) + # GIT_DIR can interfere with correct operation of Versioneer. + # It may be intended to be passed to the Versioneer-versioned project, + # but that should not change where we get our version from. + env = os.environ.copy() + env.pop("GIT_DIR", None) + runner = functools.partial(runner, env=env) + + _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, + hide_stderr=not verbose) if rc != 0: if verbose: print("Directory %s not under git control" % root) @@ -234,24 +282,57 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) + describe_out, rc = runner(GITS, [ + "describe", "--tags", "--dirty", "--always", "--long", + "--match", f"{tag_prefix}[[:digit:]]*" + ], cwd=root) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) + full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) if full_out is None: raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() - pieces = {} + pieces: Dict[str, Any] = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None + branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], + cwd=root) + # --abbrev-ref was added in git-1.6.3 + if rc != 0 or branch_name is None: + raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") + branch_name = branch_name.strip() + + if branch_name == "HEAD": + # If we aren't exactly on a branch, pick a branch which represents + # the current commit. If all else fails, we are on a branchless + # commit. + branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) + # --contains was added in git-1.5.4 + if rc != 0 or branches is None: + raise NotThisMethod("'git branch --contains' returned error") + branches = branches.split("\n") + + # Remove the first line if we're running detached + if "(" in branches[0]: + branches.pop(0) + + # Strip off the leading "* " from the list of branches. + branches = [branch[2:] for branch in branches] + if "master" in branches: + branch_name = "master" + elif not branches: + branch_name = None + else: + # Pick the first branch that is returned. Good or bad. + branch_name = branches[0] + + pieces["branch"] = branch_name + # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] # TAG might have hyphens. git_describe = describe_out @@ -268,7 +349,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # TAG-NUM-gHEX mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) if not mo: - # unparseable. Maybe git-describe is misbehaving? + # unparsable. Maybe git-describe is misbehaving? pieces["error"] = ("unable to parse git-describe output: '%s'" % describe_out) return pieces @@ -293,26 +374,27 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits + out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) + pieces["distance"] = len(out.split()) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() + date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces -def plus_or_dot(pieces): +def plus_or_dot(pieces: Dict[str, Any]) -> str: """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" -def render_pep440(pieces): +def render_pep440(pieces: Dict[str, Any]) -> str: """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you @@ -337,23 +419,71 @@ def render_pep440(pieces): return rendered -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. +def render_pep440_branch(pieces: Dict[str, Any]) -> str: + """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . + + The ".dev0" means not master branch. Note that .dev0 sorts backwards + (a feature branch will appear "older" than the master branch). Exceptions: - 1: no tags. 0.post.devDISTANCE + 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0" + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+untagged.%d.g%s" % (pieces["distance"], + pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: + """Split pep440 version string at the post-release segment. + + Returns the release segments before the post-release and the + post-release version number (or -1 if no post-release segment is present). + """ + vc = str.split(ver, ".post") + return vc[0], int(vc[1] or 0) if len(vc) == 2 else None + + +def render_pep440_pre(pieces: Dict[str, Any]) -> str: + """TAG[.postN.devDISTANCE] -- No -dirty. + + Exceptions: + 1: no tags. 0.post0.devDISTANCE + """ + if pieces["closest-tag"]: if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] + # update the post release segment + tag_version, post_version = pep440_split_post(pieces["closest-tag"]) + rendered = tag_version + if post_version is not None: + rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) + else: + rendered += ".post0.dev%d" % (pieces["distance"]) + else: + # no commits, use the tag as the version + rendered = pieces["closest-tag"] else: # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] + rendered = "0.post0.dev%d" % pieces["distance"] return rendered -def render_pep440_post(pieces): +def render_pep440_post(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards @@ -380,12 +510,41 @@ def render_pep440_post(pieces): return rendered -def render_pep440_old(pieces): +def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: + """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . + + The ".dev0" means not master branch. + + Exceptions: + 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += ".post%d" % pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "g%s" % pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0.post%d" % pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+g%s" % pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def render_pep440_old(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. - Eexceptions: + Exceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: @@ -402,7 +561,7 @@ def render_pep440_old(pieces): return rendered -def render_git_describe(pieces): +def render_git_describe(pieces: Dict[str, Any]) -> str: """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. @@ -422,7 +581,7 @@ def render_git_describe(pieces): return rendered -def render_git_describe_long(pieces): +def render_git_describe_long(pieces: Dict[str, Any]) -> str: """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. @@ -442,7 +601,7 @@ def render_git_describe_long(pieces): return rendered -def render(pieces, style): +def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: return {"version": "unknown", @@ -456,10 +615,14 @@ def render(pieces, style): if style == "pep440": rendered = render_pep440(pieces) + elif style == "pep440-branch": + rendered = render_pep440_branch(pieces) elif style == "pep440-pre": rendered = render_pep440_pre(pieces) elif style == "pep440-post": rendered = render_pep440_post(pieces) + elif style == "pep440-post-branch": + rendered = render_pep440_post_branch(pieces) elif style == "pep440-old": rendered = render_pep440_old(pieces) elif style == "git-describe": @@ -474,7 +637,7 @@ def render(pieces, style): "date": pieces.get("date")} -def get_versions(): +def get_versions() -> Dict[str, Any]: """Get version information or return default if unable to do so.""" # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have # __file__, we can work backwards from there to the root. Some @@ -495,7 +658,7 @@ def get_versions(): # versionfile_source is the relative path from the top of the source # tree (where the .git directory might live) to this file. Invert # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): + for _ in cfg.versionfile_source.split('/'): root = os.path.dirname(root) except NameError: return {"version": "0+unknown", "full-revisionid": None, diff --git a/transformato/analysis.py b/transformato/analysis.py index 2ac4edca..2f50ac9c 100644 --- a/transformato/analysis.py +++ b/transformato/analysis.py @@ -18,7 +18,7 @@ from pymbar import mbar from openmm import unit from openmm import Platform, XmlSerializer, vec3 -from openmm.app import CharmmPsfFile, Simulation +from openmm.app import CharmmPsfFile, Simulation, AmberPrmtopFile from tqdm import tqdm from transformato.helper_functions import temperature @@ -99,6 +99,11 @@ def __init__(self, configuration: dict, structure_name: str): self.thinning: int = 0 self.save_results_to_path: str = f"{self.configuration['system_dir']}/results/" self.traj_files = defaultdict(list) + ff = self.configuration["simulation"].get("forcefield") + if ff is None: + self.forcefield = "charmm" + else: + self.forcefield = ff def load_trajs(self, nr_of_max_snapshots: int = 300, multiple_runs: int = 0): """ @@ -113,30 +118,56 @@ def load_trajs(self, nr_of_max_snapshots: int = 300, multiple_runs: int = 0): ) def _generate_openMM_system(self, env: str, lambda_state: int) -> Simulation: - # read in necessary files + ### read in necessary xml (_system.xml and _integrator.xml) and topology files (charmm: psf and amber:parm7) conf_sub = self.configuration["system"][self.structure][env] file_name = f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}_system.xml" system = XmlSerializer.deserialize(open(file_name).read()) file_name = f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}_integrator.xml" integrator = XmlSerializer.deserialize(open(file_name).read()) - psf_file_path = f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}.psf" - psf = CharmmPsfFile(psf_file_path) + if self.forcefield == "charmm": + psf_file_path = f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}.psf" + psf = CharmmPsfFile(psf_file_path) + elif self.forcefield == "amber": + psf_file_path = f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}.parm7" + psf = AmberPrmtopFile(psf_file_path) # generate simulations object and set states if self.configuration["simulation"]["GPU"] == True: - platform = Platform.getPlatformByName( - "CUDA" - ) # NOTE: FIXME: this needs to be set dynamically - platformProperties = {"CudaPrecision": "mixed"} - - simulation = Simulation( - psf.topology, system, integrator, platform, platformProperties - ) - else: - platform = Platform.getPlatformByName( - "CPU" - ) # NOTE: FIXME: this needs to be set dynamically + logger.info("We are using CUDA") + platform = Platform.getPlatformByName("CUDA") simulation = Simulation(psf.topology, system, integrator, platform) + else: + try: + if self.configuration["simulation"]["GPU"].upper() == "OPENCL": + try: + logger.info( + "We are using the OpenCL platform for the analysis as specified in the yaml file" + ) + platform = Platform.getPlatformByName("OpenCL") + platformProperties = {"UseCpuPme": "true"} + simulation = Simulation( + psf.topology, + system, + integrator, + platform, + platformProperties, + ) + except: + logger.warning( + "We are falling back to CUDA as OpenCL does not workd" + ) + platform = Platform.getPlatformByName("CUDA") + simulation = Simulation( + psf.topology, system, integrator, platform + ) + elif self.configuration["simulation"]["GPU"].upper() == "CUDA": + logger.info("We are using CUDA") + platform = Platform.getPlatformByName("CUDA") + simulation = Simulation(psf.topology, system, integrator, platform) + except AttributeError: + logger.info("We are using CPU") + platform = Platform.getPlatformByName("CPU") + simulation = Simulation(psf.topology, system, integrator, platform) simulation.context.setState( XmlSerializer.deserialize( @@ -301,12 +332,8 @@ def calculate_dG_using_mbar(self, u_kn: np.array, N_k: dict, env: str): nr_of_snapshots = N_k[env][d] + N_k[env][d + 1] u_kn_ = u_kn[d : d + 2 :, start : start + nr_of_snapshots] m = mbar.MBAR(u_kn_, N_k[env][d : d + 2]) - logger.debug( - m.compute_free_energy_differences(return_dict=True)["Delta_f"][0, 1] - ) - logger.debug( - m.compute_free_energy_differences(return_dict=True)["dDelta_f"][0, 1] - ) + logger.debug(m.getFreeEnergyDifferences(return_dict=True)["Delta_f"][0, 1]) + logger.debug(m.getFreeEnergyDifferences(return_dict=True)["dDelta_f"][0, 1]) start += N_k[env][d] @@ -464,11 +491,18 @@ def energy_at_lambda( if not os.path.isfile(dcd_path): raise RuntimeError(f"{dcd_path} does not exist.") - traj = MDAnalysis.Universe( - f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}.psf", - f"{dcd_path}", - in_memory=in_memory, - ) + if self.forcefield == "charmm": + traj = MDAnalysis.Universe( + f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}.psf", + f"{dcd_path}", + in_memory=in_memory, + ) + elif self.forcefield == "amber": + traj = MDAnalysis.Universe( + f"{self.base_path}/intst{lambda_state}/{conf_sub['intermediate-filename']}.parm7", + f"{dcd_path}", + in_memory=in_memory, + ) # simple thinning of the Trajectory start = int(0.25 * len(traj.trajectory)) @@ -694,9 +728,9 @@ def _load_mbar_results(file: str): def free_energy_differences(self, env="vacuum"): """matrix of free energy differences""" try: - r = self.mbar_results[env].compute_free_energy_differences( - return_dict=True - )["Delta_f"] + r = self.mbar_results[env].getFreeEnergyDifferences(return_dict=True)[ + "Delta_f" + ] except KeyError: raise KeyError(f"Free energy difference not obtained for : {env}") return r @@ -704,7 +738,7 @@ def free_energy_differences(self, env="vacuum"): def free_energy_overlap(self, env="vacuum"): """overlap of lambda states""" try: - r = self.mbar_results[env].compute_overlap()["matrix"] + r = self.mbar_results[env].computeOverlap()["matrix"] except KeyError: raise KeyError(f"Free energy overlap not obtained for : {env}") @@ -713,9 +747,9 @@ def free_energy_overlap(self, env="vacuum"): def free_energy_difference_uncertainties(self, env="vacuum"): """matrix of asymptotic uncertainty-estimates accompanying free energy differences""" try: - r = self.mbar_results[env].compute_free_energy_differences( - return_dict=True - )["dDelta_f"] + r = self.mbar_results[env].getFreeEnergyDifferences(return_dict=True)[ + "dDelta_f" + ] except KeyError: raise KeyError(f"Free energy uncertanties not obtained for : {env}") return r diff --git a/transformato/bin/drude_openmm_run.py b/transformato/bin/drude_openmm_run.py new file mode 100644 index 00000000..97f6cd66 --- /dev/null +++ b/transformato/bin/drude_openmm_run.py @@ -0,0 +1,197 @@ +""" +File created in analogy to CHARMM-GUI (http://www.charmm-gui.org) +Last update: November, 2023 +""" + +from __future__ import print_function +import argparse +import sys +import os + +from omm_readinputs import * +from omm_readparams import * +from omm_vfswitch import * + +import openmm.unit as unit +from openmm.unit import * +from openmm import * +from openmm.app import * + +parser = argparse.ArgumentParser() +parser.add_argument("-odcd", metavar="DCDFILE", dest="odcd") +parser.add_argument("-env", metavar="ENVIRONMENT", dest="env") +args = parser.parse_args() + +# Load parameters +env = args.env +print(f"Loading parameters in this environment {env}") + + +inputs = read_inputs(f"lig_in_{env}.inp") + +if os.path.isfile(f"lig_in_{env}.parm7"): + top = AmberPrmtopFile(f"lig_in_{env}.parm7") + crd = AmberInpcrdFile(f"lig_in_{env}.rst7") + fftype = "amber" +else: + fftype = "charmm" + params = read_params("toppar.str") + top = CharmmPsfFile(f"lig_in_{env}.psf") #compatible with charmm calcs by SB + crd = read_crd(f"lig_in_{env}.crd") + top = gen_box(top, crd) + +# Build system +if env == "waterbox" or env == "complex": + nboptions = dict( + nonbondedMethod=inputs.coulomb, + nonbondedCutoff=inputs.r_off * unit.nanometers, + constraints=inputs.cons, + ewaldErrorTolerance=inputs.ewald_Tol, + ) +elif env == "vacuum": + nboptions = dict( + nonbondedMethod=NoCutoff, + constraints=inputs.cons, + ) +print(f"Applying the following nonbonded options {nboptions}") + +if inputs.vdw == "Switch" and env != "vacuum": + print(f"Setting the vdw switching function to the defalut Openmm Switch") + nboptions["switchDistance"] = inputs.r_on * unit.nanometers +if inputs.vdw == "LJPME" and env != "vacuum": + print(f"Using LJPME for the vdw long range interactions") + nboptions["nonbondedMethod"] = LJPME +if fftype == "amber": + system = top.createSystem(**nboptions) +else: + system = top.createSystem(params, **nboptions) + + +if inputs.vdw == "Force-switch" and fftype != "amber" and env != "vacuum": + print(f"Setting the vdw switching function to: Force-switch") + system = vfswitch(system, top, inputs) +if hasattr(inputs, "lj_lrc") and inputs.lj_lrc == "yes" and env != "vacuum": + print(f"We will use LJ Long range correction (LRC)") + for force in system.getForces(): + if isinstance(force, NonbondedForce): + force.setUseDispersionCorrection(True) + if ( + isinstance(force, CustomNonbondedForce) + and force.getNumTabulatedFunctions() != 1 + ): + force.setUseLongRangeCorrection(True) + +if env != "vacuum": + barostat = MonteCarloBarostat(inputs.p_ref * bar, inputs.temp * kelvin) + system.addForce(barostat) + +# integrator = LangevinIntegrator( +# inputs.temp * kelvin, 1 / unit.picosecond, inputs.dt * unit.picoseconds +# ) + +integrator = DrudeNoseHooverIntegrator( + inputs.temp * kelvin, + 10 / picosecond, + 1 * kelvin, + 200 / picosecond, + 0.0005 * picoseconds, +) + +# integrator.setMaxDrudeDistance(0.2 * angstroms) +# if integrator.getMaxDrudeDistance() == 0: +# print("No Drude Hard Wall Contraint in use") +# else: +# print("Drude Hard Wall set to {}".format(integrator.getMaxDrudeDistance())) + + +# Set platform +platform = Platform.getPlatformByName("CUDA") +prop = dict() +# Check if restraints.yaml exists - if it does, system uses restraints + +# pdbpath = args.inpfile.replace(".inp", ".pdb") + +# if os.path.exists("./restraints.yaml") and "complex" in pdbpath: +# import transformato.restraints as tfrs +# import yaml + +# print("Found restraints.yaml - applying restraints") +# # Load tiny restraints config +# with open("./restraints.yaml", "r") as stream: +# try: +# configuration = yaml.safe_load(stream) +# except yaml.YAMLError as exc: +# print(exc) + +# cc_names = configuration["system"]["structure"]["ccs"] + +# # Add forces via transformato.restraints + +# if not os.path.exists(pdbpath): +# raise FileNotFoundError( +# f"Couldnt find {pdbpath} necessary for Restraint Analysis" +# ) + +# restraintList = tfrs.create_restraints_from_config(configuration, pdbpath) + +# for restraint in restraintList: +# restraint.createForce(cc_names) +# restraint.applyForce(system) + + +# Build simulation context +simulation = Simulation(top.topology, system, integrator, platform, prop) +simulation.context.setPositions(crd.positions) +if os.path.isfile(f"lig_in_{env}.irst"): + with open(f"lig_in_{env}.irst", "r") as f: + simulation.context.setState(XmlSerializer.deserialize(f.read())) + + +# Calculate initial system energy +print("\nInitial system energy") +print(simulation.context.getState(getEnergy=True).getPotentialEnergy()) + +# Energy minimization +if inputs.mini_nstep > 0: + print("\nEnergy minimization: %s steps" % inputs.mini_nstep) + simulation.minimizeEnergy(maxIterations=inputs.mini_nstep) + print(simulation.context.getState(getEnergy=True).getPotentialEnergy()) + +# Generate initial velocities +if inputs.gen_vel == "yes": + print("\nGenerate initial velocities") + if inputs.gen_seed: + simulation.context.setVelocitiesToTemperature(inputs.gen_temp, inputs.gen_seed) + else: + simulation.context.setVelocitiesToTemperature(inputs.gen_temp) + +# Production +print("\nMD run: %s steps" % inputs.nstep) +simulation.reporters.append(DCDReporter(args.odcd, inputs.nstdcd)) +simulation.reporters.append( + StateDataReporter( + sys.stdout, + inputs.nstout, + step=True, + time=True, + potentialEnergy=True, + temperature=True, + progress=True, + remainingTime=True, + speed=True, + totalSteps=inputs.nstep, + separator="\t", + ) +) + +simulation.step(inputs.nstep) + +# needed for later analysis +file_name = f"lig_in_{env}" +state = simulation.context.getState(getPositions=True, getVelocities=True) +with open(file_name + ".rst", "w") as f: + f.write(XmlSerializer.serialize(state)) +with open(file_name + "_integrator.xml", "w") as outfile: + outfile.write(XmlSerializer.serialize(integrator)) +with open(file_name + "_system.xml", "w") as outfile: + outfile.write(XmlSerializer.serialize(system)) diff --git a/transformato/bin/openmm_run.py b/transformato/bin/openmm_run.py index 3e1fc2c0..0aa509ee 100644 --- a/transformato/bin/openmm_run.py +++ b/transformato/bin/openmm_run.py @@ -1,12 +1,6 @@ """ -Generated by CHARMM-GUI (http://www.charmm-gui.org) - -openmm_run.py - -This program is OpenMM running scripts written in python. - -Correspondance: jul316@lehigh.edu or wonpil@lehigh.edu -Last update: March 29, 2017 +File created in analogy to CHARMM-GUI (http://www.charmm-gui.org) +Last update: November, 2023 """ from __future__ import print_function @@ -17,173 +11,126 @@ from omm_readinputs import * from omm_readparams import * from omm_vfswitch import * -from omm_barostat import * -from omm_restraints import * -from omm_rewrap import * +import openmm.unit as unit from openmm.unit import * from openmm import * from openmm.app import * parser = argparse.ArgumentParser() -parser.add_argument("-i", dest="inpfile", help="Input parameter file", required=True) -parser.add_argument("-p", dest="psffile", help="Input CHARMM PSF file", required=True) -parser.add_argument("-c", dest="crdfile", help="Input CHARMM CRD file", required=True) -parser.add_argument( - "-t", dest="toppar", help="Input CHARMM-GUI toppar stream file", required=True -) -parser.add_argument( - "-b", - dest="sysinfo", - help="Input CHARMM-GUI sysinfo stream file (optional)", - default=None, -) -parser.add_argument( - "-icrst", - metavar="RSTFILE", - dest="icrst", - help="Input CHARMM RST file (optional)", - default=None, -) -parser.add_argument( - "-irst", - metavar="RSTFILE", - dest="irst", - help="Input restart file (optional)", - default=None, -) -parser.add_argument( - "-ichk", - metavar="CHKFILE", - dest="ichk", - help="Input checkpoint file (optional)", - default=None, -) -parser.add_argument( - "-opdb", - metavar="PDBFILE", - dest="opdb", - help="Output PDB file (optional)", - default=None, -) -parser.add_argument( - "-orst", - metavar="RSTFILE", - dest="orst", - help="Output restart file (optional)", - default=None, -) -parser.add_argument( - "-ochk", - metavar="CHKFILE", - dest="ochk", - help="Output checkpoint file (optional)", - default=None, -) -parser.add_argument( - "-odcd", - metavar="DCDFILE", - dest="odcd", - help="Output trajectory file (optional)", - default=None, -) -parser.add_argument( - "-rewrap", - dest="rewrap", - help="Re-wrap the coordinates in a molecular basis (optional)", - action="store_true", - default=False, -) +parser.add_argument("-odcd", metavar="DCDFILE", dest="odcd") +parser.add_argument("-env", metavar="ENVIRONMENT", dest="env") args = parser.parse_args() # Load parameters -print("Loading parameters") -inputs = read_inputs(args.inpfile) -params = read_params(args.toppar) -psf = CharmmPsfFile(args.psffile) -crd = read_crd(args.crdfile) -if args.sysinfo: - psf = read_box(psf, args.sysinfo) +env = args.env +print(f"Loading parameters in this environment {env}") + + +inputs = read_inputs(f"lig_in_{env}.inp") + +if os.path.isfile(f"lig_in_{env}.parm7"): + top = AmberPrmtopFile(f"lig_in_{env}.parm7") + crd = AmberInpcrdFile(f"lig_in_{env}.rst7") + fftype = "amber" else: - psf = gen_box(psf, crd) + fftype = "charmm" + params = read_params("toppar.str") + top = CharmmPsfFile(f"lig_in_{env}.psf") + crd = read_crd(f"lig_in_{env}.crd") + top = gen_box(top, crd) # Build system -nboptions = dict( - nonbondedMethod=inputs.coulomb, - nonbondedCutoff=inputs.r_off * nanometers, - constraints=inputs.cons, - ewaldErrorTolerance=inputs.ewald_Tol, -) - -if inputs.vdw == "Switch": - nboptions["switchDistance"] = inputs.r_on * nanometers -system = psf.createSystem(params, **nboptions) -if inputs.vdw == "Force-switch": - system = vfswitch(system, psf, inputs) +if env == "waterbox" or env == "complex": + nboptions = dict( + nonbondedMethod=inputs.coulomb, + nonbondedCutoff=inputs.r_off * unit.nanometers, + constraints=inputs.cons, + ewaldErrorTolerance=inputs.ewald_Tol, + ) +elif env == "vacuum": + nboptions = dict( + nonbondedMethod=NoCutoff, + constraints=inputs.cons, + ) +print(f"Applying the following nonbonded options {nboptions}") + +if inputs.vdw == "Switch" and env != "vacuum": + print(f"Setting the vdw switching function to the defalut Openmm Switch") + nboptions["switchDistance"] = inputs.r_on * unit.nanometers +if inputs.vdw == "LJPME" and env != "vacuum": + print(f"Using LJPME for the vdw long range interactions") + nboptions["nonbondedMethod"] = LJPME +if fftype == "amber": + system = top.createSystem(**nboptions) +else: + system = top.createSystem(params, **nboptions) + + +if inputs.vdw == "Force-switch" and fftype != "amber" and env != "vacuum": + print(f"Setting the vdw switching function to: Force-switch") + system = vfswitch(system, top, inputs) +if hasattr(inputs, "lj_lrc") and inputs.lj_lrc == "yes" and env != "vacuum": + print(f"We will use LJ Long range correction (LRC)") + for force in system.getForces(): + if isinstance(force, NonbondedForce): + force.setUseDispersionCorrection(True) + if ( + isinstance(force, CustomNonbondedForce) + and force.getNumTabulatedFunctions() != 1 + ): + force.setUseLongRangeCorrection(True) + +if env != "vacuum": + barostat = MonteCarloBarostat(inputs.p_ref * bar, inputs.temp * kelvin) + system.addForce(barostat) -system = barostat(system, inputs) -if inputs.rest == "yes": - system = restraints(system, crd, inputs) integrator = LangevinIntegrator( - inputs.temp * kelvin, inputs.fric_coeff / picosecond, inputs.dt * picoseconds + inputs.temp * kelvin, 1 / unit.picosecond, inputs.dt * unit.picoseconds ) # Set platform platform = Platform.getPlatformByName("CUDA") -prop = dict() # Check if restraints.yaml exists - if it does, system uses restraints -pdbpath = args.inpfile.replace(".inp", ".pdb") +# pdbpath = args.inpfile.replace(".inp", ".pdb") -if os.path.exists("./restraints.yaml") and "complex" in pdbpath: - import transformato.restraints as tfrs - import yaml +# if os.path.exists("./restraints.yaml") and "complex" in pdbpath: +# import transformato.restraints as tfrs +# import yaml - print("Found restraints.yaml - applying restraints") - # Load tiny restraints config - with open("./restraints.yaml", "r") as stream: - try: - configuration = yaml.safe_load(stream) - except yaml.YAMLError as exc: - print(exc) +# print("Found restraints.yaml - applying restraints") +# # Load tiny restraints config +# with open("./restraints.yaml", "r") as stream: +# try: +# configuration = yaml.safe_load(stream) +# except yaml.YAMLError as exc: +# print(exc) - cc_names = configuration["system"]["structure"]["ccs"] +# cc_names = configuration["system"]["structure"]["ccs"] - # Add forces via transformato.restraints +# # Add forces via transformato.restraints - if not os.path.exists(pdbpath): - raise FileNotFoundError( - f"Couldnt find {pdbpath} necessary for Restraint Analysis" - ) +# if not os.path.exists(pdbpath): +# raise FileNotFoundError( +# f"Couldnt find {pdbpath} necessary for Restraint Analysis" +# ) - restraintList = tfrs.create_restraints_from_config(configuration, pdbpath) +# restraintList = tfrs.create_restraints_from_config(configuration, pdbpath) - for restraint in restraintList: - restraint.createForce(cc_names) - restraint.applyForce(system) +# for restraint in restraintList: +# restraint.createForce(cc_names) +# restraint.applyForce(system) # Build simulation context -simulation = Simulation(psf.topology, system, integrator, platform, prop) +simulation = Simulation(top.topology, system, integrator, platform, prop) simulation.context.setPositions(crd.positions) -if args.icrst: - charmm_rst = read_charmm_rst(args.icrst) - simulation.context.setPositions(charmm_rst.positions) - simulation.context.setVelocities(charmm_rst.velocities) - simulation.context.setPeriodicBoxVectors( - charmm_rst.box[0], charmm_rst.box[1], charmm_rst.box[2] - ) -if args.irst: - with open(args.irst, "r") as f: +if os.path.isfile(f"lig_in_{env}.irst"): + with open(f"lig_in_{env}.irst", "r") as f: simulation.context.setState(XmlSerializer.deserialize(f.read())) -if args.ichk: - with open(args.ichk, "rb") as f: - simulation.context.loadCheckpoint(f.read()) -# Re-wrap -if args.rewrap: - simulation = rewrap(simulation) # Calculate initial system energy print("\nInitial system energy") @@ -192,9 +139,7 @@ # Energy minimization if inputs.mini_nstep > 0: print("\nEnergy minimization: %s steps" % inputs.mini_nstep) - simulation.minimizeEnergy( - tolerance=inputs.mini_Tol * kilojoule / mole, maxIterations=inputs.mini_nstep - ) + simulation.minimizeEnergy(maxIterations=inputs.mini_nstep) print(simulation.context.getState(getEnergy=True).getPotentialEnergy()) # Generate initial velocities @@ -206,48 +151,32 @@ simulation.context.setVelocitiesToTemperature(inputs.gen_temp) # Production -if inputs.nstep > 0: - print("\nMD run: %s steps" % inputs.nstep) - if inputs.nstdcd > 0: - if not args.odcd: - args.odcd = "output.dcd" - simulation.reporters.append(DCDReporter(args.odcd, inputs.nstdcd)) - simulation.reporters.append( - StateDataReporter( - sys.stdout, - inputs.nstout, - step=True, - time=True, - potentialEnergy=True, - temperature=True, - progress=True, - remainingTime=True, - speed=True, - totalSteps=inputs.nstep, - separator="\t", - ) +print("\nMD run: %s steps" % inputs.nstep) +simulation.reporters.append(DCDReporter(args.odcd, inputs.nstdcd)) +simulation.reporters.append( + StateDataReporter( + sys.stdout, + inputs.nstout, + step=True, + time=True, + potentialEnergy=True, + temperature=True, + progress=True, + remainingTime=True, + speed=True, + totalSteps=inputs.nstep, + separator="\t", ) - # Simulated annealing? - if inputs.annealing == "yes": - interval = inputs.interval - temp = inputs.temp_init - for i in range(inputs.nstep): - integrator.setTemperature(temp * kelvin) - simulation.step(1) - temp += interval - else: - simulation.step(inputs.nstep) - -# Write restart file -if not (args.orst or args.ochk): - args.orst = "output.rst" -if args.orst: - state = simulation.context.getState(getPositions=True, getVelocities=True) - with open(args.orst, "w") as f: - f.write(XmlSerializer.serialize(state)) -if args.ochk: - with open(args.ochk, "wb") as f: - f.write(simulation.context.createCheckpoint()) -if args.opdb: - crd = simulation.context.getState(getPositions=True).getPositions() - PDBFile.writeFile(psf.topology, crd, open(args.opdb, "w")) +) + +simulation.step(inputs.nstep) + +# needed for later analysis +file_name = f"lig_in_{env}" +state = simulation.context.getState(getPositions=True, getVelocities=True) +with open(file_name + ".rst", "w") as f: + f.write(XmlSerializer.serialize(state)) +with open(file_name + "_integrator.xml", "w") as outfile: + outfile.write(XmlSerializer.serialize(integrator)) +with open(file_name + "_system.xml", "w") as outfile: + outfile.write(XmlSerializer.serialize(system)) diff --git a/transformato/bin/openmm_run_vacuum.py b/transformato/bin/openmm_run_vacuum.py deleted file mode 100644 index bc52a648..00000000 --- a/transformato/bin/openmm_run_vacuum.py +++ /dev/null @@ -1,87 +0,0 @@ -import argparse - -from omm_readinputs import * -from omm_readparams import * -from openmm.unit import * -from openmm import * -from openmm.app import * - -parser = argparse.ArgumentParser() -parser.add_argument("-i", dest="inpfile", help="Input parameter file", required=True) -parser.add_argument("-p", dest="psffile", help="Input CHARMM PSF file", required=True) -parser.add_argument("-c", dest="crdfile", help="Input CHARMM CRD file", required=True) -parser.add_argument( - "-t", dest="toppar", help="Input CHARMM-GUI toppar stream file", required=True -) -parser.add_argument( - "-irst", - metavar="RSTFILE", - dest="irst", - help="Input restart file (optional)", - default=None, -) -parser.add_argument( - "-orst", - metavar="RSTFILE", - dest="orst", - help="Output restart file (optional)", - default=None, -) -parser.add_argument( - "-odcd", - metavar="DCDFILE", - dest="odcd", - help="Output trajectory file (optional)", - default=None, -) -args = parser.parse_args() - -inputs = read_inputs(args.inpfile) -params = read_params(args.toppar) -psf = CharmmPsfFile(args.psffile) -crd = read_crd(args.crdfile) - -# Build system -integrator = LangevinIntegrator( - inputs.temp * kelvin, inputs.fric_coeff / picosecond, inputs.dt * picoseconds -) - -nboptions = dict( - nonbondedMethod=NoCutoff, - constraints=inputs.cons, -) - -system = psf.createSystem(params, **nboptions) - -simulation = Simulation(psf.topology, system, integrator) -simulation.context.setPositions(crd.positions) - -print(simulation.context.getState(getEnergy=True).getPotentialEnergy()) -simulation.minimizeEnergy(maxIterations=500) -print(simulation.context.getState(getEnergy=True).getPotentialEnergy()) - -print("\nMD run: %s steps" % inputs.nstep) -simulation.reporters.append(DCDReporter(args.odcd, inputs.nstdcd)) -simulation.reporters.append( - StateDataReporter( - sys.stdout, - inputs.nstout, - step=True, - time=True, - potentialEnergy=True, - temperature=True, - progress=True, - remainingTime=True, - speed=True, - totalSteps=inputs.nstep, - separator="\t", - ) -) -simulation.step(inputs.nstep) - -if not (args.orst): - args.orst = "output.rst" -if args.orst: - state = simulation.context.getState(getPositions=True, getVelocities=True) - with open(args.orst, "w") as f: - f.write(XmlSerializer.serialize(state)) diff --git a/transformato/bin/simulation-rbfe.sh b/transformato/bin/simulation-rbfe.sh index 9341a55a..48ebb1ad 100644 --- a/transformato/bin/simulation-rbfe.sh +++ b/transformato/bin/simulation-rbfe.sh @@ -9,18 +9,10 @@ cd ${path} pwd hostname -input=lig_in_complex -init=lig_in_complex -pstep=lig_in_complex + istep=lig_in_complex -irst=lig_in_complex -orst=lig_in_complex_rst -python -u openmm_run.py -i ${input}.inp -t toppar.str -p ${init}.psf -c ${init}.crd -irst ${irst}.rst -orst ${irst} -odcd ${istep}.dcd &> complex_out.log +python openmm_run.py -env complex -odcd ${istep}.dcd &> complex_out.log + -input=lig_in_waterbox -init=lig_in_waterbox -pstep=lig_in_waterbox istep=lig_in_waterbox -irst=lig_in_waterbox -orst=lig_in_waterbox_rst -python -u openmm_run.py -i ${input}.inp -t toppar.str -p ${init}.psf -c ${init}.crd -irst ${irst}.rst -orst ${irst} -odcd ${istep}.dcd &> waterbox_out.log +python openmm_run.py -env waterbox -odcd ${istep}.dcd &> waterbox_out.log diff --git a/transformato/bin/simulation-rsfe.sh b/transformato/bin/simulation-rsfe.sh index 6ec680c6..e799e08f 100644 --- a/transformato/bin/simulation-rsfe.sh +++ b/transformato/bin/simulation-rsfe.sh @@ -3,41 +3,16 @@ path=$1 -SWITCH=$2 cd ${path} pwd hostname -export OPENMM_CPU_THREADS=4 -run_vacuum () { -input=lig_in_vacuum -init=lig_in_vacuum -pstep=lig_in_vacuum istep=lig_in_vacuum -irst=lig_in_vacuum -orst=lig_in_vacuum_rst -python -u openmm_run_vacuum.py -i ${input}.inp -t toppar.str -p ${init}.psf -c ${init}.crd -orst ${irst}.rst -odcd ${istep}.dcd &> vacuum_out.log -} - -run_waterbox () { -input=lig_in_waterbox -init=lig_in_waterbox -pstep=lig_in_waterbox +python openmm_run.py -env vacuum -odcd ${istep}.dcd &> vacuum_out.log + + + istep=lig_in_waterbox -irst=lig_in_waterbox -orst=lig_in_waterbox_rst -python -u openmm_run.py -i ${input}.inp -t toppar.str -p ${init}.psf -c ${init}.crd -orst ${irst}.rst -odcd ${istep}.dcd &> waterbox_out.log -} - - -case ${SWITCH} in -1) -run_vacuum -;; -2) -run_vacuum -run_waterbox -;; -esac +python openmm_run.py -env waterbox -odcd ${istep}.dcd &> waterbox_out.log diff --git a/transformato/mutate.py b/transformato/mutate.py index 2fecec32..b45c0e2c 100644 --- a/transformato/mutate.py +++ b/transformato/mutate.py @@ -27,6 +27,7 @@ logger = logging.getLogger(__name__) +logging.getLogger().setLevel(logging.DEBUG) def _flattened(list_of_lists: list) -> list: @@ -58,7 +59,7 @@ def _performe_linear_cc_scaling( for lambda_value in np.linspace(1, 0, nr_of_steps + 1)[1:]: print("####################") print( - f"Perform paramteter scaling on cc in step: {intermediate_factory.current_step} with lamb: {lambda_value}" + f"Perform parameter scaling on cc in step: {intermediate_factory.current_step} with lamb: {lambda_value}" ) print("####################") intermediate_factory.write_state( @@ -197,7 +198,7 @@ def perform_mutations( and configuration["simulation"]["free-energy-type"] == "asfe" ): for lambda_value in np.linspace( - 0.75, 0, nr_of_mutation_steps_lj_of_heavy_atoms + 1 + 0.5, 0, nr_of_mutation_steps_lj_of_heavy_atoms + 1 ): print("####################") print( @@ -358,7 +359,7 @@ def __init__( self.dummy_region_cc2: DummyRegion self.asfe: bool = False - self._check_cgenff_versions() + # self._check_cgenff_versions() except: logger.info( @@ -638,7 +639,6 @@ def _check_for_lp( for atom in psf.view[f":{tlc}"].atoms: if atom.name.find("LP") == False: - print(f"die Atome {atom}") if atom.frame_type.atom1.idx in flat_ordered_connected_dummy_regions: lp_dict_dummy_region[atom.frame_type.atom1.idx].append(atom.idx) @@ -871,6 +871,13 @@ def _prepare_cc_for_charge_transfer(self): [self.get_common_core_idx_mol1(), self.get_common_core_idx_mol2()], [self.dummy_region_cc1, self.dummy_region_cc2], ): + ## We need this for point mutations, because if we give a resid, the mol here + ## consists only of on residue which resid is always 1 + try: + int(tlc) + tlc = "1" + except ValueError: + tlc = tlc # set `initial_charge` parameter for Mutation for atom in psf.view[f":{tlc}"].atoms: # charge, epsilon and rmin are directly modiefied @@ -1474,8 +1481,13 @@ def _mutate_to_common_core( """ mutations = defaultdict(list) - tlc = self.s1_tlc - + ## We need this for point mutations, because if we give a resid, the mol here + ## consists only of on residue which resid is always 1 + try: + int(self.s1_tlc) + tlc = "1" + except ValueError: + tlc = self.s1_tlc if self.asfe: psf = self.psf1["waterbox"] cc_idx = [] # no CC in ASFE @@ -1496,7 +1508,13 @@ def _mutate_to_common_core( logger.info(f"Terminal dummy atoms: {list_termin_dummy_atoms}") if mol_name == "m2": - tlc = self.s2_tlc + ## We need this for point mutations, because if we give a resid, the mol here + ## consists only of on residue which resid is always 1 + try: + int(self.s2_tlc) + tlc = "1" + except ValueError: + tlc = self.s2_tlc # iterate through atoms and select atoms that need to be mutated atoms_to_be_mutated = [] @@ -1565,7 +1583,11 @@ def _mutate_to_common_core( steric_mutation_to_default=True, ) mutations["default-lj"].append(m) - elif atom_idx in hydrogens or psf[atom_idx].type == "LPH": + elif ( + atom_idx in hydrogens + or psf[atom_idx].type.startswith("LP") + or psf[atom_idx].type.startswith("DRUD") + ): # already mutated continue else: @@ -1654,8 +1676,6 @@ def _get_atom_mapping(self) -> dict: cc_names_struc1.append(ligand1_atom.name) cc_names_struc2.append(ligand2_atom.name) - print(f"CC Struc1: {cc_names_struc1}") - print(f"CC Struc2: {cc_names_struc2}") return match_atom_names_cc1_to_cc2 def _mutate_charges(self, psf: pm.charmm.CharmmPsfFile, scale: float): @@ -1742,6 +1762,20 @@ def _mutate_atoms(self, psf: pm.charmm.CharmmPsfFile, lambda_value: float): ligand1_atom.mod_type = mod_type( modified_epsilon, modified_rmin ) + # do this only when using GAFF + if type(psf) == pm.amber.AmberParm: + assert ( + psf[f":{self.tlc_cc1}@{ligand1_atom.idx+1}"] + .atoms[0] + .name + == ligand1_atom.name + ) + pm.tools.actions.changeLJSingleType( + psf, + f":{self.tlc_cc1}@{ligand1_atom.idx+1}", + modified_rmin, + modified_epsilon, + ).execute() if not found: raise RuntimeError("No corresponding atom in cc2 found") @@ -1810,6 +1844,16 @@ def _mutate_bonds(self, psf: pm.charmm.CharmmPsfFile, lambda_value: float): ligand1_bond.mod_type = mod_type(modified_k, modified_req) logger.debug(ligand1_bond.mod_type) + # do this only when using GAFF + if type(psf) == pm.amber.AmberParm: + pm.tools.actions.setBond( + psf, + f":{self.tlc_cc1}@{ligand1_bond.atom1.idx+1}", + f":{self.tlc_cc1}@{ligand1_bond.atom2.idx+1}", + modified_k, + modified_req, + ).execute() + if not found: logger.critical(ligand1_bond) raise RuntimeError( @@ -1884,6 +1928,17 @@ def _mutate_angles(self, psf: pm.charmm.CharmmPsfFile, lambda_value: float): cc1_angle.mod_type = mod_type(modified_k, modified_theteq) + # do this only when using GAFF + if type(psf) == pm.amber.AmberParm: + pm.tools.actions.setAngle( + psf, + f":{self.tlc_cc1}@{cc1_angle.atom1.idx+1}", + f":{self.tlc_cc1}@{cc1_angle.atom2.idx+1}", + f":{self.tlc_cc1}@{cc1_angle.atom3.idx+1}", + modified_k, + modified_theteq, + ).execute() + if not found: logger.critical(cc1_angle) raise RuntimeError("No corresponding angle in cc2 found") @@ -1964,7 +2019,16 @@ def _mutate_torsions(self, psf: pm.charmm.CharmmPsfFile, lambda_value: float): f = max((1 - ((1 - lambda_value) * 2)), 0.0) if f > 0.0 or lambda_value == 0.5: - for torsion_t in original_torsion.type: + ## Necessary, because in Amber topologies this is not a list + if ( + type(original_torsion.type) + == pm.topologyobjects.DihedralType + ): + orig_torsion_as_list = [original_torsion.type] + else: + orig_torsion_as_list = original_torsion.type + + for torsion_t in orig_torsion_as_list: modified_phi_k = torsion_t.phi_k * f mod_types.append( mod_type( @@ -1979,7 +2043,14 @@ def _mutate_torsions(self, psf: pm.charmm.CharmmPsfFile, lambda_value: float): # torsion present at cc2 needs to be fully turned on at lambda_value == 0.0 f = 1 - min((lambda_value) * 2, 1.0) if f > 0.0: - for torsion_t in new_torsion.type: + + ## Necessary, because in Amber topologies this is not a list + if type(new_torsion.type) == pm.topologyobjects.DihedralType: + new_torsion_as_list = [new_torsion.type] + else: + new_torsion_as_list = new_torsion.type + + for torsion_t in new_torsion_as_list: modified_phi_k = torsion_t.phi_k * f if modified_phi_k >= 0.0: mod_types.append( @@ -1994,6 +2065,21 @@ def _mutate_torsions(self, psf: pm.charmm.CharmmPsfFile, lambda_value: float): original_torsion.mod_type = mod_types + # do this only when using GAFF + if type(psf) == pm.amber.AmberParm: + pm.tools.actions.addDihedral( + psf, + f":{self.tlc_cc1}@{original_torsion.atom1.idx+1}", + f":{self.tlc_cc1}@{original_torsion.atom2.idx+1}", + f":{self.tlc_cc1}@{original_torsion.atom3.idx+1}", + f":{self.tlc_cc1}@{original_torsion.atom4.idx+1}", + modified_phi_k, + torsion_t.per, + torsion_t.phase, + torsion_t.scnb, + torsion_t.scee, + ).execute() + if not found: logger.critical(original_torsion) raise RuntimeError("No corresponding torsion in cc2 found") @@ -2008,8 +2094,11 @@ def mutate(self, psf: pm.charmm.CharmmPsfFile, lambda_value: float): lambda_value : float lambda_value """ + try: + assert type(psf) == pm.charmm.CharmmPsfFile + except AssertionError: + assert type(psf) == pm.amber.AmberParm - assert type(psf) == pm.charmm.CharmmPsfFile if self.charge_mutation: logger.info(f" -- Charge parameters from cc1 are transformed to cc2.") logger.info(f"Lambda value:{lambda_value}") @@ -2051,8 +2140,10 @@ def __init__(self, atoms_to_be_mutated: list, dummy_region: DummyRegion): def _mutate_charge( self, psf: pm.charmm.CharmmPsfFile, lambda_value: float, offset: int ): - total_charge = int( - round(sum([atom.initial_charge for atom in psf.view[f":{self.tlc}"].atoms])) + total_charge = float( + round( + sum([atom.initial_charge for atom in psf.view[f":{self.tlc}"].atoms]), 4 + ), ) # scale the charge of all atoms print(f"Scaling charge on: {self.atoms_to_be_mutated}") @@ -2065,6 +2156,16 @@ def _mutate_charge( atom.charge = atom.initial_charge * lambda_value logger.debug(f"New charge: {atom.charge}") + # in the end, we save the topology for amber (lig_in_env.parm7) using parmed + # pm.save_parm(), this requires all changes applied via an action tool + if type(psf) == pm.amber.AmberParm: + pm.tools.actions.change( + psf, + "CHARGE", + f":{self.tlc}@{idx+1}", + atom.initial_charge * lambda_value, + ).execute() + # check to avoid compensating charges when doing asfe if ( lambda_value != 1 @@ -2081,6 +2182,9 @@ def _mutate_vdw( offset: int, to_default: bool, ): + """ + This is used to scale the LJ parameters of the DDD and DDX atoms to zero in phase II and III + """ if not set(vdw_atom_idx).issubset(set(self.atoms_to_be_mutated)): raise RuntimeError( f"Specified atom {vdw_atom_idx} is not in atom_idx list {self.atoms_to_be_mutated}. Aborting." @@ -2096,13 +2200,23 @@ def _mutate_vdw( atom_type_suffix = "DDX" atom.rmin = 1.5 atom.epsilon = -0.15 + # do this only when using GAFF + if type(psf) == pm.amber.AmberParm: + assert psf[f":{self.tlc}@{atom.idx+1}"].atoms[0].name == atom.name + pm.tools.actions.changeLJSingleType( + psf, + f":{self.tlc}@{atom.idx+1}", + 1.5, + 0.15, ### ATTENTION: This should be -0.15 but somehow GAFF does not like negative values + ).execute() + else: logger.info("Mutate to dummy") atom_type_suffix = f"DDD" - self._scale_epsilon(atom, lambda_value) - self._scale_rmin(atom, lambda_value) + self._scale_epsilon_and_rmin(atom, lambda_value, psf, self.tlc) + # NOTEthere is always a type change - self._modify_type(atom, psf, atom_type_suffix) + self._modify_type(atom, psf, atom_type_suffix, self.tlc) def mutate( self, @@ -2123,7 +2237,12 @@ def mutate( logger.debug(f"LJ scaling factor: {lambda_value_electrostatic}") logger.debug(f"VDW scaling factor: {lambda_value_vdw}") - offset = min([a.idx for a in psf.view[f":{self.tlc.upper()}"].atoms]) + try: + offset = min([a.idx for a in psf.view[f":{self.tlc.upper()}"].atoms]) + ### This give a ValueErrror for point mutation, where a resid is specified + ### but here we have only one ligand or the residue, which should be mutated left + except ValueError: + offset = min([a.idx for a in psf.view[f":1"].atoms]) if lambda_value_electrostatic < 1.0: self._mutate_charge(psf, lambda_value_electrostatic, offset) @@ -2203,30 +2322,44 @@ def _compensate_charge( connecting_real_atom_for_this_dummy_region ) - # check if rest charge is missing + #### check if rest charge is missing new_charge = sum( [atom.charge for atom in psf.view[f":{self.tlc.upper()}"].atoms] ) - if not (np.isclose(new_charge, total_charge, rtol=1e-4)): + if not (np.isclose(round(new_charge, 3), round(total_charge, 3), rtol=1e-4)): raise RuntimeError( f"Charge compensation failed. Introducing non integer total charge: {new_charge}. Target total charge: {total_charge}." ) @staticmethod - def _scale_epsilon(atom, lambda_value: float): + def _scale_epsilon_and_rmin(atom, lambda_value, psf, tlc): + """ + This scales the LJ interactions (epsilon and rmin) from non-interacting DDD atom (no charge) + to 'real' dummy atom (no LJ!), typically this is performed in one step, but to be sure + we offer scalling possibility here as well + """ logger.debug(atom) logger.debug(atom.initial_epsilon) - atom.epsilon = atom.initial_epsilon * lambda_value - - @staticmethod - def _scale_rmin(atom, lambda_value: float): - logger.debug(atom) logger.debug(atom.initial_rmin) + + atom.epsilon = atom.initial_epsilon * lambda_value atom.rmin = atom.initial_rmin * lambda_value + ### do this only when using GAFF + if type(psf) == pm.amber.AmberParm: + # Quick check, if selected atom via AMBER mask is the same as the atom + # we want to modify + assert psf[f":{tlc}@{atom.idx+1}"].atoms[0].type == atom.type + pm.tools.actions.addLJType( + psf, + f":{tlc}@{atom.idx+1}", + radius=atom.initial_rmin * lambda_value, + epsilon=atom.initial_epsilon * lambda_value, + ).execute() + @staticmethod - def _modify_type(atom, psf, atom_type_suffix: str): + def _modify_type(atom, psf, atom_type_suffix, tlc): if hasattr(atom, "initial_type"): # only change parameters pass @@ -2240,3 +2373,11 @@ def _modify_type(atom, psf, atom_type_suffix: str): new_type = f"{atom_type_suffix}{psf.mutations_to_default}" atom.type = new_type + + if type(psf) == pm.amber.AmberParm: + pm.tools.actions.change( + psf, + "AMBER_ATOM_TYPE", + f":{tlc}@{atom.idx+1}", + new_type, + ).execute() diff --git a/transformato/state.py b/transformato/state.py index f6972cdc..0026ba40 100644 --- a/transformato/state.py +++ b/transformato/state.py @@ -46,6 +46,10 @@ def __init__( self.output_files = [] self.current_step = 1 self.multiple_runs = multiple_runs + try: + self.drude: bool = configuration["simulation"]["drude"] + except KeyError: + self.drude: bool = False def endstate_correction(self): logger.info(f"Will create script for endstate correction") @@ -92,6 +96,50 @@ def endstate_correction(self): fin.close() fout.close() + def _write_amber_files( + self, psf: pm.amber.AmberParm, output_file_base: str, tlc: str, env: str + ): + """ + Write a parm7 and rst7 file for each intermediate step, including information about the dummy atoms + """ + if env == "waterbox": + psf.write_parm(f"{output_file_base}/lig_in_{env}.parm7") + psf.write_rst7(f"{output_file_base}/lig_in_{env}.rst7") + if env == "complex": + psf.write_parm(f"{output_file_base}/lig_in_{env}.parm7") + psf.write_rst7(f"{output_file_base}/lig_in_{env}.rst7") + elif env == "vacuum": + psf[f":{tlc}"].write_parm(f"{output_file_base}/lig_in_{env}.parm7") + psf[f":{tlc}"].write_rst7(f"{output_file_base}/lig_in_{env}.rst7") + ### This is only necessary, because we create the parm7 and rst7 by slicing the corresponding waterbox + ### In this case there is one flag left which tells openmm when reading in the parm7 file, that there is + ### a box (PBC). For that reason we have to manually set this flag to False (0). + lines_left = 0 + with open(f"{output_file_base}/lig_in_{env}.parm7", "r") as file: + with open( + f"{output_file_base}/lig_in_{env}_temp.parm7", "w" + ) as tempFile: + for line in file: + if line.startswith("%FLAG POINTERS"): + lines_left = 6 + if lines_left > 0: + lines_left -= 1 + if lines_left == 1: + newLine = line[:63] + "0" + line[64:] + assert ( + line.split()[7] == "1" + ) # in this position it is usually 1 indicating a box, if we change it to 0, openmm thinks there is no box (see: https://ambermd.org/FileFormats.php#topo.cntrl) + tempFile.write(newLine) + else: + tempFile.write(line) + else: + tempFile.write(line) + + shutil.move(tempFile.name, file.name) + + else: + logger.critical(f"Environment {env} not supported") + def write_state( self, mutation_conf: List, @@ -123,7 +171,8 @@ def write_state( for mutation_type in mutation_conf: if ( common_core_transformation < 1.0 - ): # NOTE: THis is inconsisten -- the mutatino_type is the actual mutation in this case + ): # NOTE: THis is inconsistent -- the mutatino_type is the actual mutation in this case + # This happens only for one ligand and starts the process of changing cc1 into cc2 mutation_type.mutate( psf=self.system.psfs[env], lambda_value=common_core_transformation, @@ -138,7 +187,6 @@ def write_state( atoms_to_be_mutated=mutation_type.atoms_to_be_mutated, dummy_region=mutation_type.dummy_region, ) - mutator.mutate( psf=self.system.psfs[env], lambda_value_electrostatic=lambda_value_electrostatic, @@ -146,10 +194,24 @@ def write_state( vdw_atom_idx=mutation_type.vdw_atom_idx, steric_mutation_to_default=mutation_type.steric_mutation_to_default, ) - self._write_psf(self.system.psfs[env], output_file_base, env) - self._write_rtf_file(self.system.psfs[env], output_file_base, self.system.tlc) - self._write_prm_file(self.system.psfs[env], output_file_base, self.system.tlc) - self._write_toppar_str(output_file_base) + if self.system.ff == "amber": + # needed for each environment + self._write_amber_files( + self.system.psfs[env], output_file_base, self.system.tlc, env + ) + elif self.system.ff == "charmm": + self._write_psf(self.system.psfs[env], output_file_base, env) + + if self.system.ff == "charmm": + # needed only once per intermediate state + self._write_rtf_file( + self.system.psfs[env], output_file_base, self.system.tlc + ) + self._write_prm_file( + self.system.psfs[env], output_file_base, self.system.tlc + ) + self._write_toppar_str(output_file_base) + self._copy_files(output_file_base) # Create run folder for dcd output for each intst state @@ -176,21 +238,6 @@ def write_state( self.current_step += 1 - def _add_serializer(self, file): - # adding serializer functions - with open(file, "a") as f: - f.write( - """ -# mw: adding xml serializer to the simulation script -file_name = str(args.psffile).replace('.psf', '') -print(file_name) -with open(file_name + '_integrator.xml','w') as outfile: - outfile.write(XmlSerializer.serialize(integrator)) -with open(file_name + '_system.xml','w') as outfile: - outfile.write(XmlSerializer.serialize(system)) -""" - ) - def _get_simulations_parameters(self): prms = {} for key in self.configuration["simulation"]["parameters"]: @@ -341,21 +388,24 @@ def _copy_charmm_files(self, intermediate_state_file_path: str): # copy diverse set of helper files for CHARMM for env in self.system.envs: - if env != "vacuum": - FILES = [ - "crystal_image.str", - "step3_pbcsetup.str", - ] - for f in FILES: - try: - charmm_source = f"{basedir}/{env}/{f}" - charmm_target = ( - f"{intermediate_state_file_path}/charmm_{env}_{f}" - ) - shutil.copyfile(charmm_source, charmm_target) - except FileNotFoundError: - logger.critical(f"Could not find file: {f}") - raise + if env != "vacuum" and self.system.ff.lower() != "amber": + try: + FILES = [ + "crystal_image.str", + "step3_pbcsetup.str", + ] + for f in FILES: + try: + charmm_source = f"{basedir}/{env}/{f}" + charmm_target = ( + f"{intermediate_state_file_path}/charmm_{env}_{f}" + ) + shutil.copyfile(charmm_source, charmm_target) + except FileNotFoundError: + logger.critical(f"Could not find file: {f}") + raise + except: + logger.info("") # copy rst files rst_file_source = f"{basedir}/{env}/{self.configuration['system'][self.system.structure][env]['rst_file_name']}.rst" @@ -363,7 +413,7 @@ def _copy_charmm_files(self, intermediate_state_file_path: str): try: shutil.copyfile(rst_file_source, rst_file_target) except FileNotFoundError: - logger.warning( + logger.info( f"No restart file found for {env} -- starting simulation from crd file." ) @@ -375,11 +425,11 @@ def _modify_submit_script(self, shFile): fout = open(f"{shFile}.tmp", "wt") with open(f"{shFile}", "r+") as f: for line in f: - if line.startswith(f"input=lig_in_"): + if line.startswith(f"istep=lig_in_"): fout.write("for i in {1.." + f"{self.multiple_runs}" + "};\n") fout.write("do \n") fout.write(line) - elif line.startswith("python -u openmm"): + elif line.startswith("python openmm"): line = line.replace("${istep}.dcd", "run_${i}/${istep}.dcd") fout.write( line.replace( @@ -480,13 +530,9 @@ def _copy_omm_files(self, intermediate_state_file_path: str): # copy diverse set of helper functions for openMM FILES = [ - "omm_barostat.py", "omm_readinputs.py", "omm_readparams.py", - "omm_restraints.py", - "omm_rewrap.py", "omm_vfswitch.py", - "omm_hmr.py", ] for f in FILES: try: @@ -497,32 +543,20 @@ def _copy_omm_files(self, intermediate_state_file_path: str): logger.critical(f"Could not find file: {f}") # copy omm simulation script - # start with waterbox - omm_simulation_script_source = f"{self.configuration['bin_dir']}/openmm_run.py" + if self.drude: + omm_simulation_script_source = f"{self.configuration['bin_dir']}/drude_openmm_run.py" # ATTENTION: NEEDS TO BE MERGED IN THE FUTURE + else: + omm_simulation_script_source = ( + f"{self.configuration['bin_dir']}/openmm_run.py" + ) + omm_simulation_script_target = f"{intermediate_state_file_path}/openmm_run.py" shutil.copyfile(omm_simulation_script_source, omm_simulation_script_target) # add serialization self._check_hmr(omm_simulation_script_target) - self._add_serializer(omm_simulation_script_target) self._change_platform(omm_simulation_script_target) check_switching_function(self.vdw_switch) - if ( - self.configuration["simulation"]["free-energy-type"] == "rsfe" - or self.configuration["simulation"]["free-energy-type"] == "asfe" - ): - # add vacuum scripts - omm_simulation_script_source = ( - f"{self.configuration['bin_dir']}/openmm_run_vacuum.py" - ) - omm_simulation_script_target = ( - f"{intermediate_state_file_path}/openmm_run_vacuum.py" - ) - shutil.copyfile(omm_simulation_script_source, omm_simulation_script_target) - self._check_hmr(omm_simulation_script_target) - self._add_serializer(omm_simulation_script_target) - self._change_platform(omm_simulation_script_target) - def _check_hmr(self, file): "add hmr if requested in config file" if self.configuration["simulation"].get("HMR", False): @@ -544,34 +578,60 @@ def _change_platform(self, file): f = open(file, "r") g = open(f"{file}_tmp", "w+") i = 0 # counting lines - - if self.configuration["simulation"]["GPU"]: - logger.debug("Preparing for CUDA") - for line in f.readlines(): - if "# Set platform" in line and i == 0: - i += 1 - g.write(line) - elif i == 1: - i += 1 - g.write("platform = Platform.getPlatformByName('CUDA')\n") - elif i == 2: - i += 2 - g.write("prop = dict(CudaPrecision='mixed')\n") - else: - g.write(line) - else: - for line in f.readlines(): - if "# Set platform" in line and i == 0: - i += 1 - g.write(line) - elif i == 1: - i += 1 - g.write("platform = Platform.getPlatformByName('CPU')\n") - elif i == 2: - i += 2 - g.write("prop = dict()\n") - else: - g.write(line) + try: + if self.configuration["simulation"]["GPU"].upper() == "OPENCL": + for line in f.readlines(): + if "# Set platform" in line and i == 0: + i += 1 + g.write(line) + elif i == 1: + i += 1 + g.write("platform = Platform.getPlatformByName('OpenCL')\n") + elif i == 2: + i += 2 + g.write("prop = dict(UseCpuPme='true')\n") + else: + g.write(line) + elif self.configuration["simulation"]["GPU"].upper() == "CUDA": + for line in f.readlines(): + if "# Set platform" in line and i == 0: + i += 1 + g.write(line) + elif i == 1: + i += 1 + g.write("platform = Platform.getPlatformByName('CUDA')\n") + elif i == 2: + i += 2 + g.write("prop = dict()\n") + else: + g.write(line) + except AttributeError: + if self.configuration["simulation"]["GPU"] == True: + for line in f.readlines(): + if "# Set platform" in line and i == 0: + i += 1 + g.write(line) + elif i == 1: + i += 1 + g.write("platform = Platform.getPlatformByName('CUDA')\n") + elif i == 2: + i += 2 + g.write("prop = dict()\n") + else: + g.write(line) + else: + for line in f.readlines(): + if "# Set platform" in line and i == 0: + i += 1 + g.write(line) + elif i == 1: + i += 1 + g.write("platform = Platform.getPlatformByName('CPU')\n") + elif i == 2: + i += 2 + g.write("prop = dict()\n") + else: + g.write(line) f.close() g.close() @@ -580,6 +640,7 @@ def _change_platform(self, file): def _copy_ligand_specific_top_and_par( self, basedir: str, intermediate_state_file_path: str ): + # copy ligand rtf file ligand_rtf = f"{basedir}/waterbox/{self.system.tlc.lower()}/{self.system.tlc.lower()}_g.rtf" toppar_target = ( @@ -595,10 +656,14 @@ def _copy_ligand_specific_top_and_par( def _copy_ligand_specific_str( self, basedir: str, intermediate_state_file_path: str ): - # copy ligand rtf file - ligand_rtf = f"{basedir}/waterbox/{self.system.tlc.lower()}/{self.system.tlc.lower()}.str" - toppar_target = f"{intermediate_state_file_path}/{self.system.tlc.lower()}.str" - shutil.copyfile(ligand_rtf, toppar_target) + # If the tlc is no name, we assume that there is no str/rtf file (as for point mutations in RNAs) + if not self.drude: + # copy ligand rtf file + ligand_rtf = f"{basedir}/waterbox/{self.system.tlc.lower()}/{self.system.tlc.lower()}.str" + toppar_target = ( + f"{intermediate_state_file_path}/{self.system.tlc.lower()}.str" + ) + shutil.copyfile(ligand_rtf, toppar_target) def _copy_crd_file(self, intermediate_state_file_path: str): basedir = self.system.charmm_gui_base @@ -622,16 +687,19 @@ def _copy_files(self, intermediate_state_file_path: str): basedir = self.system.charmm_gui_base - try: - self._copy_ligand_specific_top_and_par( - basedir, intermediate_state_file_path - ) - except: - self._copy_ligand_specific_str(basedir, intermediate_state_file_path) + if self.system.ff.lower() == "charmm": + try: + self._copy_ligand_specific_top_and_par( + basedir, intermediate_state_file_path + ) + except: + self._copy_ligand_specific_str(basedir, intermediate_state_file_path) # copy crd file - self._copy_crd_file((intermediate_state_file_path)) - + try: + self._copy_crd_file((intermediate_state_file_path)) + except: + pass # copy openMM and charmm specific scripts self._copy_omm_files(intermediate_state_file_path) self._copy_charmm_files(intermediate_state_file_path) @@ -698,21 +766,27 @@ def _overwrite_simulation_script_parameters( ) logger.critical(f"###################") - for l in input_simulation_parameter.readlines(): - if l.strip(): - t1, t2_comment = [e.strip() for e in l.split("=")] - t2, comment = [e.strip() for e in t2_comment.split("#")] - comment = comment.strip() - if t1 in overwrite_parameters.keys(): - t2 = overwrite_parameters[t1] - del overwrite_parameters[t1] # remove from dict - if t1 == "vdw": - t2 = t2.capitalize() - output_simulation_parameter.write( - f"{t1:<25} = {t2:<25} # {comment:<30}\n" - ) - else: - output_simulation_parameter.write("\n") + try: + for l in input_simulation_parameter.readlines(): + if l.strip(): + t1, t2_comment = [e.strip() for e in l.split("=")] + t2, comment = [e.strip() for e in t2_comment.split("#")] + comment = comment.strip() + if t1 in overwrite_parameters.keys(): + t2 = overwrite_parameters[t1] + del overwrite_parameters[t1] # remove from dict + if t1 == "vdw": + t2 = t2.capitalize() + output_simulation_parameter.write( + f"{t1:<25} = {t2:<25} # {comment:<30}\n" + ) + else: + output_simulation_parameter.write("\n") + except ValueError: + logger.critical( + f"The original inp {input_simulation_parameter.name} file contains a line without a comment " + ) + raise SystemExit # set parameters that have no equivalent in the pregenerated parameter file for t1 in overwrite_parameters.keys(): @@ -767,7 +841,9 @@ def _write_prm_file(self, psf, output_file_base, tlc): view = psf.view[f":{tlc}"] # writing atom parameters for atom in view.atoms: - if hasattr(atom, "initial_type"): + if hasattr(atom, "initial_type") and atom.type != "DRUD": + # if hasattr(atom, "initial_type") and not atom.type.startswith("D"): + if set([atom.type]) in already_seen: continue else: @@ -794,7 +870,31 @@ def _write_prm_file(self, psf, output_file_base, tlc): already_seen = [] for bond in view.bonds: atom1, atom2 = bond.atom1, bond.atom2 - if any(hasattr(atom, "initial_type") for atom in [atom1, atom2]): + if atom1.type == "DRUD" or atom2.type == "DRUD": + pass + elif ( + # atom1.type == "DRUD" + # or atom2.type == "DRUD" + atom1.type.startswith("LP") + or atom2.type.startswith("LP") + ): + if any(hasattr(atom, "initial_type") for atom in [atom1, atom2]): + if set([atom1.type, atom2.type]) in already_seen: + continue + else: + already_seen.append(set([atom1.type, atom2.type])) + logger.debug( + "{:7} {:7} {:9.5f} {:9.5f} \n".format( + str(atom1.type), str(atom2.type), 0, 0 + ) + ) + prm_file_handler.write( + "{:7} {:7} {:9.5f} {:9.5f} \n".format( + str(atom1.type), str(atom2.type), 0, 0 + ) + ) + + elif any(hasattr(atom, "initial_type") for atom in [atom1, atom2]): if set([atom1.type, atom2.type]) in already_seen: continue else: @@ -1050,6 +1150,17 @@ def _write_toppar_str(self, output_file_base): ../../toppar/toppar_all36_lipid_model.str ../../toppar/toppar_all36_lipid_prot.str ../../toppar/toppar_all36_lipid_sphingo.str +../../toppar/toppar_all36_na_rna_modified.str +""" + toppar_dir = f"{self.path}/../toppar" + + if os.path.isdir(toppar_dir): + pass + else: + toppar_dir = get_toppar_dir() + + if os.path.isfile(f"{toppar_dir}/toppar_drude_main_protein_2023a_flex.str"): + toppar_format += f"""../../toppar/toppar_drude_main_protein_2023a_flex.str """ if os.path.isfile( f"{self.system.charmm_gui_base}/waterbox/{self.system.tlc.lower()}/{self.system.tlc.lower()}_g.rtf" @@ -1059,10 +1170,18 @@ def _write_toppar_str(self, output_file_base): dummy_atom_definitions.rtf dummy_parameters.prm """ - else: + elif not self.drude and ( + os.path.isfile( + f"{self.system.charmm_gui_base}/waterbox/{self.system.tlc.lower()}/{self.system.tlc.lower()}.str" + ) + ): toppar_format += f"""{self.system.tlc.lower()}.str dummy_atom_definitions.rtf dummy_parameters.prm +""" + else: + toppar_format += f"""dummy_atom_definitions.rtf +dummy_parameters.prm """ f = open(f"{output_file_base}/toppar.str", "w+") diff --git a/transformato/system.py b/transformato/system.py index ed22a2d5..d6c3066a 100644 --- a/transformato/system.py +++ b/transformato/system.py @@ -30,26 +30,55 @@ def __init__(self, configuration: dict, structure: str): self.name: str = configuration["system"][structure]["name"] self.tlc: str = configuration["system"][structure]["tlc"] self.charmm_gui_base: str = configuration["system"][structure]["charmm_gui_dir"] - self.psfs: defaultdict = defaultdict(pm.charmm.CharmmPsfFile) self.offset: defaultdict = defaultdict(int) - self.parameter = self._read_parameters("waterbox") - self.cgenff_version: float self.envs = set() + + try: + self.drude: bool = configuration["simulation"]["drude"] + except KeyError: + self.drude: bool = False + + try: + self.ff: str = str.lower(configuration["simulation"]["forcefield"]) + self.psfs: defaultdict = defaultdict(pm.amber.AmberParm) + except KeyError: + self.ff: str = "charmm" + self.psfs: defaultdict = defaultdict(pm.charmm.CharmmPsfFile) + self.parameter = self._read_parameters( + "waterbox" + ) # not sure if this is really needed + self.cgenff_version: float + # running a binding-free energy calculation? if configuration["simulation"]["free-energy-type"] == "rbfe": self.envs = set(["complex", "waterbox"]) - for env in self.envs: - parameter = self._read_parameters(env) - # set up system - self.psfs[env] = self._initialize_system(configuration, env) - # load parameters - self.psfs[env].load_parameters(parameter) - # get offset - self.offset[ - env - ] = self._determine_offset_and_set_possible_dummy_properties( - self.psfs[env] - ) + + if self.ff == "charmm": + for env in self.envs: + parameter = self._read_parameters(env) + # set up system + self.psfs[env] = self._initialize_system(configuration, env) + # load parameters + self.psfs[env].load_parameters(parameter) + # get offset + self.offset[env] = ( + self._determine_offset_and_set_possible_dummy_properties( + self.psfs[env] + ) + ) + elif self.ff == "amber": + for env in self.envs: + self.psfs[env] = pm.load_file( + f"{self.charmm_gui_base}/{env}/openmm/step3_input.parm7" + ) + self.psfs[env].load_rst7( + f"{self.charmm_gui_base}/{env}/openmm/step3_input.rst7" + ) + self.offset[env] = ( + self._determine_offset_and_set_possible_dummy_properties( + self.psfs[env] + ) + ) # generate rdkit mol object of small molecule self.mol: Chem.Mol = self._generate_rdkit_mol( @@ -63,17 +92,32 @@ def __init__(self, configuration: dict, structure: str): ): self.envs = set(["waterbox", "vacuum"]) for env in self.envs: - parameter = self._read_parameters(env) - # set up system - self.psfs[env] = self._initialize_system(configuration, env) - # load parameters - self.psfs[env].load_parameters(parameter) - # get offset - self.offset[ - env - ] = self._determine_offset_and_set_possible_dummy_properties( - self.psfs[env] - ) + if self.ff == "charmm": + parameter = self._read_parameters(env) + # set up system + self.psfs[env] = self._initialize_system(configuration, env) + # load parameters + self.psfs[env].load_parameters(parameter) + self.offset[env] = ( + self._determine_offset_and_set_possible_dummy_properties( + self.psfs[env] + ) + ) + + elif self.ff == "amber": + self.psfs[env] = pm.load_file( + f"{self.charmm_gui_base}/waterbox/openmm/step3_input.parm7" + ) + self.psfs[env].load_rst7( + f"{self.charmm_gui_base}/waterbox/openmm/step3_input.rst7" + ) + self.offset[env] = ( + self._determine_offset_and_set_possible_dummy_properties( + self.psfs[env] + ) + ) + # if env == "vacuum": + # self.psfs["vacuum"] = self.psfs["waterbox"][f":{self.tlc}"] # generate rdkit mol object of small molecule self.mol: Chem.Mol = self._generate_rdkit_mol( @@ -181,7 +225,7 @@ def _read_parameters(self, env: str) -> pm.charmm.CharmmParameterSet: ) # check cgenff versions - if parameter_files: + if parameter_files and self.ff == "charmm": with open(parameter_files[0]) as f: _ = f.readline() cgenff = f.readline().rstrip() @@ -201,6 +245,11 @@ def _read_parameters(self, env: str) -> pm.charmm.CharmmParameterSet: parameter_files += ( f"{toppar_dir}/toppar_all36_prot_na_combined.str", ) # if modified aminoacids are needed + parameter_files += (f"{toppar_dir}/toppar_water_ions.str",) + if os.path.isfile(f"{toppar_dir}/toppar_drude_main_protein_2023a_flex.str"): + parameter_files += ( + f"{toppar_dir}/toppar_drude_main_protein_2023a_flex.str", + ) if os.path.isfile(f"{toppar_dir}/toppar_all36_moreions.str"): parameter_files += (f"{toppar_dir}/toppar_all36_moreions.str",) # set up parameter objec @@ -255,17 +304,28 @@ def _initialize_system( # which is necessary for the check_for_lp function if lp: g = psf.groups + oldFlags = psf.flags frame_idx = [] frame_frame = [] + prop_idx = [] + properties = [] for atom in psf.atoms: if hasattr(atom, "frame_type"): frame_idx.append(atom.idx) frame_frame.append(atom.frame_type) + for atom in psf.atoms: + if hasattr(atom, "props"): + prop_idx.append(atom.idx) + properties.append(atom.props) psf = psf[f":{self.tlc}"] # the important part psf.groups = g + psf.flags = oldFlags for atom in psf.atoms: if atom.idx in frame_idx: atom.frame_type = frame_frame[frame_idx.index(atom.idx)] + for atom in psf.atoms: + if atom.idx in prop_idx: + atom.props = properties[prop_idx.index(atom.idx)] else: psf = psf[f":{self.tlc}"] @@ -298,7 +358,11 @@ def _determine_offset_and_set_possible_dummy_properties( Returns ---------- """ - assert type(psf) == pm.charmm.CharmmPsfFile + if self.ff == "amber": + assert type(psf) == pm.amber._amberparm.AmberParm + else: + assert type(psf) == pm.charmm.CharmmPsfFile + if len(psf.view[f":{self.tlc}"].atoms) < 1: raise RuntimeError(f"No ligand selected for tlc: {self.tlc}") @@ -350,6 +414,40 @@ def _return_small_molecule(self, env: str) -> Chem.rdchem.Mol: "Could not load small molecule sdf file in {charmm_gui_env}. Aborting." ) + def _create_sdf_from_pdb(self, psf: pm.topologyobjects): + """ + This function creates a sdf file from the file provided in openmm/step3_input.pdb + and reads in this sdf file. This should now have the same order as the psf topology object + and is from now on used as the rdkit mol object. + + Parameters + ---------- + psf: pm.topologyobjects + a topology provided by parmed (either CHARMM type or AMBER) + Returns + ---------- + mol : rdkit.Chem.rdchem.Mol + mol object + """ + + file_path = f"{self.charmm_gui_base}/waterbox/openmm/" + psf.save(f"{file_path}/step3_input_reordered.pdb", overwrite=True) + + from openbabel import openbabel + + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("pdb", "sdf") + mol = openbabel.OBMol() + obConversion.ReadFile(mol, f"{file_path}/step3_input_reordered.pdb") + obConversion.WriteFile(mol, f"{file_path}/step3_input_reduced.sdf") + + suppl = Chem.SDMolSupplier( + f"{file_path}/step3_input_reduced.sdf", removeHs=False + ) + mol = next(suppl) + + return mol + def _generate_rdkit_mol( self, env: str, psf: pm.charmm.CharmmPsfFile ) -> Chem.rdchem.Mol: @@ -365,46 +463,57 @@ def _generate_rdkit_mol( mol: rdkit.Chem.rdchem.Mol """ - assert type(psf) == pm.charmm.CharmmPsfFile - mol = self._return_small_molecule(env) - ( - atom_idx_to_atom_name, - _, - atom_name_to_atom_type, - atom_idx_to_atom_partial_charge, - ) = self.generate_atom_tables_from_psf(psf) + try: + mol = self._return_small_molecule(env) - for atom in mol.GetAtoms(): - atom.SetProp("atom_name", atom_idx_to_atom_name[atom.GetIdx()]) - atom.SetProp( - "atom_type", - atom_name_to_atom_type[atom_idx_to_atom_name[atom.GetIdx()]], - ) - atom.SetProp("atom_index", str(atom.GetIdx())) - atom.SetProp( - "atom_charge", str(atom_idx_to_atom_partial_charge[atom.GetIdx()]) - ) + except FileNotFoundError: + + mol = self._create_sdf_from_pdb(psf) + + mol = self.generate_atom_tables_from_psf(psf, mol) # check if psf and sdf have same indeces - for a in mol.GetAtoms(): - if str(psf[a.GetIdx()].element_name) == str(a.GetSymbol()): - pass - else: - raise RuntimeError("PSF to mol conversion did not work! Aborting.") + if not self.drude: + try: + for a in mol.GetAtoms(): + if str(psf[a.GetIdx()].element_name) == str(a.GetSymbol()): + pass + else: + raise RuntimeError( + "First PSF to mol conversion did not work, trying it with the pdb file" + ) + except RuntimeError: + # It's possible, that there is a sdf file in the TCL folder but the order does not match + # in thuis case, we try to create a matching sdf file by using the pdb file in the openmm folder + logger.info( + f"It seems like the sdf file provided in the {self.tlc} does not have the correct order, trying it again by using the pdb file" + ) + mol = self._create_sdf_from_pdb(psf) + mol = self.generate_atom_tables_from_psf(psf, mol) - return mol + # final check if psf and sdf have same indeces + for a in mol.GetAtoms(): + if str(psf[a.GetIdx()].element_name) == str(a.GetSymbol()): + pass + else: + raise RuntimeError( + "PSF to mol conversion did not work! Remove the TLC.sdf file in the tlc folder and try again!" + ) + + return mol def generate_atom_tables_from_psf( - self, psf: pm.charmm.CharmmPsfFile - ) -> Tuple[dict, dict, dict, dict]: + self, psf: pm.charmm.CharmmPsfFile, mol: Chem.rdchem.Mol + ) -> Chem.rdchem.Mol: """ Generate mapping dictionaries for a molecule in a psf. Parameters ---------- - psf: pm.charmm.CharmmPsfFile + psf: pm.charmm.CharmmPsfFile or parmed.amber._amberparm.AmberParm Returns ---------- - dict's + mol: Chem.rdchem.Mol + mol object with atom name and type properties """ atom_idx_to_atom_name = dict() @@ -412,7 +521,15 @@ def generate_atom_tables_from_psf( atom_name_to_atom_type = dict() atom_idx_to_atom_partial_charge = dict() - for atom in psf.view[f":{self.tlc}"].atoms: + ## We need this for point mutations, because if we give a resid, the mol here + ## consists only of on residue which resid is always 1 + try: + int(self.tlc) + tlc = "1" + except ValueError: + tlc = self.tlc + + for atom in psf.view[f":{tlc}"].atoms: atom_name = atom.name atom_index = atom.idx atom_type = atom.type @@ -423,9 +540,15 @@ def generate_atom_tables_from_psf( atom_name_to_atom_type[atom_name] = atom_type atom_idx_to_atom_partial_charge[atom_index] = atom_charge - return ( - atom_idx_to_atom_name, - atom_name_to_atom_idx, - atom_name_to_atom_type, - atom_idx_to_atom_partial_charge, - ) + for atom in mol.GetAtoms(): + atom.SetProp("atom_name", atom_idx_to_atom_name[atom.GetIdx()]) + atom.SetProp( + "atom_type", + atom_name_to_atom_type[atom_idx_to_atom_name[atom.GetIdx()]], + ) + atom.SetProp("atom_index", str(atom.GetIdx())) + atom.SetProp( + "atom_charge", str(atom_idx_to_atom_partial_charge[atom.GetIdx()]) + ) + + return mol diff --git a/transformato/tests/test_alchemical_path_generation.py b/transformato/tests/test_alchemical_path_generation.py index 12c3ad5d..743f1851 100644 --- a/transformato/tests/test_alchemical_path_generation.py +++ b/transformato/tests/test_alchemical_path_generation.py @@ -114,7 +114,7 @@ def test_generate_alchemical_path_for_toluene_commmon_core_with_CUDA(): i += 1 elif i == 2: print(line) - assert "dict(CudaPrecision='mixed')" in line + assert "dict()" in line i += 1 diff --git a/transformato/tests/test_amber.py b/transformato/tests/test_amber.py new file mode 100644 index 00000000..6a7408bf --- /dev/null +++ b/transformato/tests/test_amber.py @@ -0,0 +1,192 @@ +from transformato import ( + load_config_yaml, + SystemStructure, + IntermediateStateFactory, + ProposeMutationRoute, +) +from transformato.mutate import perform_mutations +from transformato.utils import postprocessing, get_test_output_dir +from transformato_testsystems.testsystems import get_testsystems_dir +import pytest +import os + + +@pytest.mark.rbfe +@pytest.mark.charmm +@pytest.mark.skipif( + os.getenv("CI") == "true", + reason="Skipping tests that cannot pass in github actions", +) +def test_full_amber_test(): + molecule = "ethane-methanol" + + configuration = load_config_yaml( + config=f"/site/raid3/johannes/amber_tests/data/config/{molecule}_amber.yaml", + input_dir="/site/raid3/johannes/amber_tests/data/", + output_dir="/site/raid3/johannes/amber_tests/", + ) + + s1 = SystemStructure(configuration, "structure1") + s2 = SystemStructure(configuration, "structure2") + s1_to_s2 = ProposeMutationRoute(s1, s2) + s1_to_s2.propose_common_core() + s1_to_s2.finish_common_core() + + mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1() + i = IntermediateStateFactory( + system=s1, + configuration=configuration, + ) + perform_mutations( + configuration=configuration, + i=i, + mutation_list=mutation_list, + nr_of_mutation_steps_charge=2, + nr_of_mutation_steps_cc=2, + ) + + mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol2() + print(mutation_list.keys()) + i = IntermediateStateFactory( + system=s2, + configuration=configuration, + ) + + perform_mutations( + configuration=configuration, + i=i, + mutation_list=mutation_list, + nr_of_mutation_steps_charge=2, + ) + + +@pytest.mark.skipif( + os.getenv("CI") == "true", + reason="Skipping tests that cannot pass in github actions", +) +def test_asfe_amber_test(): + molecule = "ethane-methanol_amber" + + configuration = load_config_yaml( + config=f"/site/raid3/johannes/amber_tests/data/config/{molecule}.yaml", + input_dir="/site/raid3/johannes/amber_tests/data/", + output_dir="/site/raid3/johannes/amber_tests/", + ) + + s1 = SystemStructure(configuration, "structure1") + s2 = SystemStructure(configuration, "structure2") + s1_to_s2 = ProposeMutationRoute(s1, s2) + s1_to_s2.propose_common_core() + s1_to_s2.finish_common_core() + + mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1() + i = IntermediateStateFactory( + system=s1, + configuration=configuration, + multiple_runs=3, + ) + perform_mutations( + configuration=configuration, + i=i, + mutation_list=mutation_list, + nr_of_mutation_steps_charge=3, + ) + mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol2() + i = IntermediateStateFactory( + system=s2, + configuration=configuration, + multiple_runs=3, + ) + perform_mutations( + configuration=configuration, + i=i, + mutation_list=mutation_list, + nr_of_mutation_steps_charge=3, + ) + + +@pytest.mark.rbfe +@pytest.mark.charmm +@pytest.mark.skipif( + os.getenv("CI") == "true", + reason="Skipping tests that cannot pass in github actions", +) +def test_amber_analysis(): + molecule = "ethanol" + configuration = load_config_yaml( + config=f"/site/raid3/johannes/amber_tests/data/config/{molecule}_asfe.yaml", + input_dir="/site/raid3/johannes/amber_tests/data/", + output_dir="/site/raid3/johannes/amber_tests/", + ) + + ddG_openMM, dddG, f_openMM = postprocessing( + configuration, + name="ethanol_amber", + engine="openMM", + max_snapshots=10000, + num_proc=6, + analyze_traj_with="mda", + show_summary=True, + multiple_runs=2, + ) + + print(f"Free energy is {ddG_openMM} +- {dddG} kT") + + +@pytest.mark.charmm +@pytest.mark.skipif( + os.getenv("CI") == "true", + reason="Skipping tests that cannot pass in github actions", +) +def test_amber_rbfe(): + + molecule = "jmc_28_ejm_31" + configuration = load_config_yaml( + config=f"/site/raid3/johannes/amber_tests/data/config/{molecule}.yaml", + input_dir="/site/raid3/johannes/amber_tests/data/", + output_dir="/site/raid3/johannes/amber_tests/", + ) + + # molecule = "1_cano-1_U" + # configuration = load_config_yaml( + # config=f"/site/raid3/johannes/amber_tests/data_GU/config/{molecule}.yaml", + # input_dir="/site/raid3/johannes/amber_tests/data_GU/", + # output_dir="/site/raid3/johannes/amber_tests/", + # ) + + s1 = SystemStructure(configuration, "structure1") + s2 = SystemStructure(configuration, "structure2") + s1_to_s2 = ProposeMutationRoute(s1, s2) + + s1_to_s2.propose_common_core() + + # # s1_to_s2.add_idx_to_common_core_of_mol1([31]) + # # s1_to_s2.add_idx_to_common_core_of_mol2([30, 31]) + + s1_to_s2.finish_common_core() + + mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol1() + i = IntermediateStateFactory( + system=s1, + configuration=configuration, + multiple_runs=3, + ) + perform_mutations( + configuration=configuration, + i=i, + mutation_list=mutation_list, + nr_of_mutation_steps_charge=3, + ) + + mutation_list = s1_to_s2.generate_mutations_to_common_core_for_mol2() + i = IntermediateStateFactory( + system=s2, + configuration=configuration, + multiple_runs=3, + ) + perform_mutations( + configuration=configuration, + i=i, + mutation_list=mutation_list, + nr_of_mutation_steps_charge=3, + ) diff --git a/transformato/tests/test_drude.py b/transformato/tests/test_drude.py new file mode 100644 index 00000000..2b34ffcc --- /dev/null +++ b/transformato/tests/test_drude.py @@ -0,0 +1,67 @@ +from transformato.utils import ( + run_simulation, + postprocessing, + get_test_output_dir, + load_config_yaml, +) +from transformato.mutate import ProposeMutationRoute, perform_mutations +from transformato.system import SystemStructure +from transformato.state import IntermediateStateFactory +import pytest +import os + + +@pytest.mark.skipif( + os.getenv("CI") == "true", + reason="Skipping tests that cannot pass in github actions", +) +def test_create_asfe_system(): + configuration = load_config_yaml( + config=f"/site/raid5/marvin/drude_test/data/config/acetamide.yaml", + input_dir=f"/site/raid5/marvin/drude_test/data/", + output_dir=f"/site/raid5/marvin/drude_test", + ) + + s1 = SystemStructure(configuration, "structure1") + s1_absolute = ProposeMutationRoute(s1) + s1_absolute.propose_common_core() + s1_absolute.finish_common_core() + mutation_list = s1_absolute.generate_mutations_to_common_core_for_mol1() + + multiple_runs = 3 + i = IntermediateStateFactory( + system=s1, multiple_runs=multiple_runs, configuration=configuration + ) + + perform_mutations( + configuration=configuration, + nr_of_mutation_steps_charge=5, + i=i, + mutation_list=mutation_list, + ) + + +@pytest.mark.skipif( + os.getenv("CI") == "true", + reason="Skipping tests that cannot pass in github actions", +) +def test_analyze_drude(): + + configuration = load_config_yaml( + config=f"/site/raid5/marvin/drude_test/data/config/methanol.yaml", + input_dir=f"/site/raid5/marvin/drude_test/data/", + output_dir=f"/site/raid5/marvin/drude_test", + ) + + ddG_openMM, dddG, _ = postprocessing( + configuration, + name="methanol", + engine="openMM", + max_snapshots=50, + num_proc=6, + analyze_traj_with="mda", + show_summary=True, + multiple_runs=1, + ) + + print(f"Free energy is {ddG_openMM} +- {dddG} kT") diff --git a/transformato/tests/test_misc.py b/transformato/tests/test_misc.py index 6d89cf1e..ea97cff0 100644 --- a/transformato/tests/test_misc.py +++ b/transformato/tests/test_misc.py @@ -1,6 +1,7 @@ """ Unit and regression test for the transformato package. """ + from transformato.helper_functions import temperature from openmm import unit import numpy as np diff --git a/transformato/tests/test_postprocessing.py b/transformato/tests/test_postprocessing.py index 8f906578..f4c326a8 100644 --- a/transformato/tests/test_postprocessing.py +++ b/transformato/tests/test_postprocessing.py @@ -1,6 +1,7 @@ """ Unit and regression test for the transformato package. """ + import os import numpy as np diff --git a/transformato/tests/test_restraints.py b/transformato/tests/test_restraints.py index ff3f4df4..43a5c6c5 100644 --- a/transformato/tests/test_restraints.py +++ b/transformato/tests/test_restraints.py @@ -10,6 +10,7 @@ Tests are mainly based on 2OJ9 """ + import glob import logging import os diff --git a/transformato/toppar/toppar_drude_main_protein_2023a_flex.str b/transformato/toppar/toppar_drude_main_protein_2023a_flex.str new file mode 100644 index 00000000..eb8c930e --- /dev/null +++ b/transformato/toppar/toppar_drude_main_protein_2023a_flex.str @@ -0,0 +1,8505 @@ +* DRUDE main topology and parameter stream file +* Includes water, 2013 +* Ions updated, June 2018 +* Nucleic acid/carbohydrate/lipid update January 2017 +* Opt molecular ions, fylin 2018 +* Halogen and NBFIX terms, fylin 2018 +* Updated protein FF with opt alpha/Thole, fylin 2018 +* 2023 version following phospholipid 2023 update +* + +!! SB: switching this to flexible format -- all MASS statements need to be replicated (ATOMS card) in the para section!!! + +ioformat extended + +!This file must be streamed prior to additional Drude FF toppar stream files +!and it includes parameters for the model compounds (toppar_drude_model*.str) + +! note use of D for second character to indicate Drude +! polarizable FF (be careful of Cadmium: use CDM) +! Parameter labeling after ! +! RESName, generic compound name of model compound followed by additional comments +! for example ! BENZ, benzene, based on crystal survey data +!Formatting information +!RTF section: please use the following format for future residues, including the spacing +!(and please clean a few up of the residues not in this format if you so desire....) +!RESI ALA 0.000 +!ATOM N ND2A2 -0.427 ALPHA -1.056 THOLE 0.711 +!BOND A1 A2 A3 A4 A5 A6 A7 A8 +!IMPR A1 A2 A3 A4 +!CMAP A1 A2 A3 A4 A1 A2 A3 A4 +!LONEPAIR relative A1 A2 A3 A4 distance 0.30 angle 91.00 dihe 180.00 +!ANISOTROPY A1 A2 A3 A4 A11 0.6968 A22 1.2194 +!IC A1 A2 A3 A4 1.3474 124.31 180.00 114.26 0.9979 + +!parameter section +!bond +!CD32E OD30A 360.00 1.415 ! comment +!angles +!HDA1A CD31A CD31A 34.50 110.10 ! comment +!HDA1A CD31A CD31A 34.50 110.10 22.53 2.1790 ! comment +!dihedrals +!CD2O1A ND2A2 CD31C CD2O2A 0.000 3 180.00 ! comment +!impropers +!CD2O1A CD31A ND2A2 OD2C1A 120.000 0 0.00 ! comment +!nonbond (LJ) +!HDW 0.0 -0.0000 0.0000 ! comment +!nbfix +!CD30A ODW -0.00500 4.04699 ! comment + +!ioformat extended + +read rtf card flex !append +* Topology for drude water, ions and proteins +* +46 + +!pre 2020 nucleic acid types, temporarily in the 2023 main file +!to be removed once the update nucleic acid parameters are put to use +MASS -1 OD2C2C 15.99940 O ! carboxylate O, anionic (phosphate), nucleic acids +MASS -1 OD30BN 15.99940 O ! ester oxygen (phosphate), nucleic acid +MASS -1 PD1AN 30.974000 P ! phosphorus, (DMP), nucleic acids +! +MASS -1 HDP1A 1.00800 H ! polar H, general +MASS -1 HDP1B 1.00800 H ! polar H, ammonium cations +MASS -1 HDP1C 1.00800 H ! polar H, aldehyde +MASS -1 HDA1A 1.00800 H ! aliphatic H, (-CH), general +MASS -1 HDA1C 1.00800 H ! aliphatic H, (-CH), special case for ammonium cations +MASS -1 HDA1R5 1.00800 H ! aliphatic H, (-CH), 5-membered ring +MASS -1 HDA2A 1.00800 H ! aliphatic H, (-CH2), general +MASS -1 HDA2C 1.00800 H ! aliphatic H, (-CH2), special case for ammonium cations +MASS -1 HDA2E 1.00800 H ! aliphatic H, (-CH2), ethers +MASS -1 HDA2R5 1.00800 H ! aliphatic H, (-CH2), 5-membered ring +MASS -1 HDA3A 1.00800 H ! aliphatic H, (-CH3), general +MASS -1 HDA3B 1.00800 H ! aliphatic H, (-CH3), special case for methanol +MASS -1 HDA3C 1.00800 H ! aliphatic H, (-CH3), special case for ammonium cations +MASS -1 HDR5A 1.00800 H ! 5-membered ring, HG and HD2 in imidazole +MASS -1 HDR5B 1.00800 H ! 5-membered ring, HE1 in imidazole +MASS -1 HDR5C 1.00800 H ! 5-membered ring, H on carbon adjacent to N in pyrrole +MASS -1 HDR5D 1.00800 H ! 5-membered ring, HG and HD2 in imidazolium +MASS -1 HDR5E 1.00800 H ! 5-membered ring, HE1 in imidazolium +MASS -1 HDR6A 1.00800 H ! aromatic H, 6-membered ring, general +MASS -1 HDR6B 1.00800 H ! aromatic H, 6-membered ring, adjacent to N (pyridine) +MASS -1 HDR6C 1.00800 H ! aromatic H, 6-membered ring, between 2 N's (pyrimidine) +MASS -1 HD2C1A 1.00800 H ! internal alkene H +MASS -1 HD2C1B 1.00800 H ! terminal alkene H +MASS -1 HDW 1.00800 H ! water H, SWM4 and SWM6 +MASS -1 CD2C1A 12.01100 C ! alkene C, internal alkene C, single unsaturation +MASS -1 CD2C1B 12.01100 C ! alkene C, terminal alkene C +MASS -1 CD2O1A 12.01100 C ! carbonyl C, amide +MASS -1 CD2O1C 12.01100 C ! carbonyl C, aldehyde +MASS -1 CD2O1D 12.01100 C ! carbonyl C, ketone +MASS -1 CD2O2A 12.01100 C ! carboxylate C, anionic +MASS -1 CD2O3A 12.01100 C ! carbonyl C, in esters and acids (neutral) +MASS -1 CD2O4A 12.01100 C ! carbonyl C, nucleic acid bases +MASS -1 CD2N1A 12.01100 C ! guanidinium C +MASS -1 CD2R5A 12.01100 C ! 5-membered ring, CG and CD2 in imidazole +MASS -1 CD2R5B 12.01100 C ! 5-membered ring, CE1 in imidazole +MASS -1 CD2R5C 12.01100 C ! 5-membered ring, pyrole, adjacent to N +MASS -1 CD2R5D 12.01100 C ! 5-membered ring, CG and CD2 in imidizolium +MASS -1 CD2R5E 12.01100 C ! 5-membered ring, CE1 in imidizolium +MASS -1 CD2R5F 12.01100 C ! C8, nucleic acid purine bases +MASS -1 CD2R6A 12.01100 C ! aromatic C, 6-membered ring +MASS -1 CD2R6B 12.01100 C ! aromatic C, 6-membered ring, adjacent to N (pyridine) +MASS -1 CD2R6C 12.01100 C ! aromatic C, 6-membered ring, between 2 heteroatoms (pyrimidine) +MASS -1 CD2R6D 12.01100 C ! aromatic C, 6-membered ring, bridging far from N (indole) +MASS -1 CD2R6F 12.01100 C ! aromatic C, 6-membered ring, bridging adjacent to N7 (purine) +MASS -1 CD2R6H 12.01100 C ! C6, nucleic acid pyrmidine bases +MASS -1 CD2R6J 12.01100 C ! C5, nucleic acid pyrmidine bases +MASS -1 CD2R6I 12.01100 C ! aromatic C, 6-membered ring, adjacent to anionic O phenolate +MASS -1 CD30A 12.01100 C ! aliphatic sp3 C, 0 H +MASS -1 CD30FA 12.01100 C ! aliphatic sp3 C, 1 H, furanoses, anomeric C1 +MASS -1 CD31A 12.01100 C ! aliphatic sp3 C, 1 H +MASS -1 CD31C 12.01100 C ! aliphatic sp3 C, 1 H, special case for carbons adjacent to esters/amides +MASS -1 CD31DC 12.01100 C ! for D-amino acids, jal +MASS -1 CD31FA 12.01100 C ! aliphatic sp3 C, 1 H, furanoses, anomeric C1 +MASS -1 CD31FB 12.01100 C ! aliphatic sp3 C, 1 H, furanoses, C2,C3 +MASS -1 CD31FC 12.01100 C ! aliphatic sp3 C, 1 H, furanoses, C4 +MASS -1 CD31G 12.01100 C ! aliphatic sp3 C, 1 H, glycerol, xhe +MASS -1 CD315A 12.01100 C ! aliphatic sp3 C, 1 H, ether, 5-memberd ring, CPNM +MASS -1 CD315B 12.01100 C ! aliphatic sp3 C, 1 H, ether, 5-memberd ring, TF2M +MASS -1 CD316A 12.01100 C ! aliphatic sp3 C, 1 H, 6-membered ring +MASS -1 CD31HA 12.01100 C ! aliphatic sp3 C, 1 H, hexopyranoses, C1 anomeric carbon, dpatel +MASS -1 CD31HB 12.01100 C ! aliphatic sp3 C, 1 H, hexopyranoses, C2, C3 and C4 +MASS -1 CD31HC 12.01100 C ! aliphatic sp3 C, 1 H, hexopyranoses, C5 +!======atom type added for glycopetide and modified carbohydrate======ahaile==08/08/2021 +MASS -1 CD30HA 12.01100 C ! aliphatic sp3 C, 1 H, hexopyranoses +MASS -1 CD32HB 12.01100 C ! aliphatic sp3 C, 1 H, hexopyranoses +MASS -1 CD32HC 12.01100 C ! aliphatic sp3 C, 1 H, hexopyranoses +!====================================================================== +MASS -1 CD32A 12.01100 C ! aliphatic sp3 C, 2 H +MASS -1 CD32B 12.01100 C ! aliphatic sp3 C, 2 H, added for GLU and phosphoglycerol lipids, from CD32A +MASS -1 CD32C 12.01100 C ! aliphatic sp3 C, 2 H, special case for carbons adjacent to esters/amides +MASS -1 CD32E 12.01100 C ! aliphatic sp3 C, 2 H, ether, for CH2 adjacent to O in linear ethers +MASS -1 CD32F 12.01100 C ! aliphatic sp3 C, 2 H, ethylene glycol, glycerol, xhe +MASS -1 CD325A 12.01100 C ! aliphatic sp3 C, 2 H, 5-membered ring +MASS -1 CD325B 12.01100 C ! aliphatic sp3 C, 2 H, ether, 5-membered ring, THF +MASS -1 CD326A 12.01100 C ! aliphatic sp3 C, 2 H, 6-membered ring +MASS -1 CD326B 12.01100 C ! aliphatic sp3 C, 2 H, ether, 6-membered ring, THP +MASS -1 CD33A 12.01100 C ! aliphatic sp3 C, 3 H +!!MODEL unique +MASS -1 CD33B 12.01100 C ! aliphatic sp3 C, 3 H, special case for methanol +!! +MASS -1 CD33C 12.01100 C ! aliphatic sp3 C, 3 H, special case for C adjacent to carbonyls/estersphosphate +MASS -1 CD33E 12.01100 C ! aliphatic sp3 C, 3 H, special case for CH3 adjacent to O in linear ethers + +MASS -1 ND2A1 14.00700 N ! amide, primary (ACEM) +MASS -1 ND2A2 14.00700 N ! amide, secondary (NMA, peptide bond) +MASS -1 ND2A3 14.00700 N ! amide, tertiary (DMA) +MASS -1 ND2B1 14.00700 N ! amine, primary (NA bases) +MASS -1 ND2R5A 14.00700 N ! neutral his protonated ring nitrogen +MASS -1 ND2R5B 14.00700 N ! neutral his unprotonated ring nitrogen +MASS -1 ND2R5C 14.00700 N ! positive his protonated ring nitrogen +MASS -1 ND2R5D 14.00700 N ! aromatic N, 5-membered, nucleic acid purine bases +MASS -1 ND2R5E 14.00700 N ! neutral unprotonated ring nitrogen, nucleic acid purine bases +MASS -1 ND2R5F 14.00700 N ! N9, nucleic acid guanine base +MASS -1 ND2R6A 14.00700 N ! aromatic N, 6-membered ring (pyridine) +MASS -1 ND2R6B 14.00700 N ! aromatic N, 6-membered ring (pyrimidine, N-C-N connectivity) +MASS -1 ND2R6C 14.00700 N ! aromatic N, 6-membered ring: protonated: nucleic acid pyrimidine bases +MASS -1 ND2R6D 14.00700 N ! N1, nucleic acid thymine base +MASS -1 ND2P1A 14.00700 N ! protonated sp2 nitrogen: guanidinium +MASS -1 ND3P2A 14.00700 N ! protonated sp3 nitrogen, 0, 1 or 2 Hs +MASS -1 ND3P3A 14.00700 N ! protonated sp3 nitrogen, 3 or 4 Hs (includes ammonia) +MASS -1 ND3A2 14.00700 N ! neutral aliphatic amines +MASS -1 ND3A3 14.00700 N ! imino nitrogen, proline + +MASS -1 OD2C1A 15.99940 O ! carbonyl O, amides +MASS -1 OD2C1B 15.99940 O ! carbonyl O, NA bases +MASS -1 OD2C1C 15.99940 O ! carbonyl O, aldehyde +MASS -1 OD2C1D 15.99940 O ! carbonyl O, ketone +MASS -1 OD2C2A 15.99940 O ! carboxylate O, anionic (acetate) +MASS -1 OD2C2B 15.99940 O ! carboxylate O, anionic (phosphate), lipids +MASS -1 OD2C3A 15.99940 O ! carbonyl O, neutral (esters) +MASS -1 OD30A 15.99940 O ! ether oxygen +MASS -1 OD30B 15.99940 O ! ester oxygen (phosphate), lipid & nucleic acids +MASS -1 OD30BR 15.99940 O ! ester oxygen (phosphate), RNA specific +MASS -1 OD30C 15.99940 O ! ester oxygen (esters) +MASS -1 OD30D 15.99940 O ! ester oxygen (terminal phosphate), MP_1 +MASS -1 OD30E 15.99940 O ! ionized hydroxyl oxygen, PHET (phenolate) +MASS -1 OD305A 15.99940 O ! ether oxygen, 5-membered ring (tetrahydrofuran) +MASS -1 OD306A 15.99940 O ! ether oxygen, 6-membered ring (tetrahydropyran) +MASS -1 OD31A 15.99940 O ! hydroxyl oxygen +MASS -1 OD31B 15.99940 O ! hydroxyl oxygen, special case for long, primary alcohols +MASS -1 OD31C 15.99940 O ! hydroxyl oxygen, phenol +MASS -1 OD31D 15.99940 O ! hydroxyl oxygen, methylphosphate +MASS -1 OD31E 15.99940 O ! hydroxyl oxygen, ethylene glycol, glycerol, xhe +MASS -1 OD31F 15.99940 O ! hydroxyl oxygen, acids +MASS -1 OD31G 15.99940 O ! hydroxyl oxygen, to resolve DNA/RNA 3TER conflict, jal +MASS -1 ODW 15.99940 O ! water oxygen, SWM4 +MASS -1 ODW6 15.99940 O ! water oxygen, SWM6 +! phosphorous +MASS -1 PD1A 30.974000 P ! phosphorus, (DMP), lipids +! Sulfurs +MASS -1 SD1A 32.06000 S ! sulfate ion, based on PD1A, a&a +MASS -1 SD31A 32.06000 S ! MESH +MASS -1 SD31B 32.06000 S ! ETSH +MASS -1 SD30A 32.06000 S ! EMS, DMS +MASS -1 SD30B 32.06000 S ! DMDS +MASS -1 SD2C2A 32.06000 S ! MES, thiolates +MASS -1 SD2C2B 32.06000 S ! ETS, thiolates + +! Monovalent ions +MASS -1 LID 6.94120 Li ! Lithium +MASS -1 POTD 39.10200 K ! Potassium +MASS -1 SODD 23.00000 Na ! Sodium +MASS -1 RBD 85.46783 Rb ! Rubidium +MASS -1 CSD 132.90545 Cs ! Caesium +MASS -1 FAD 18.99840 F ! Fluoride +MASS -1 CLAD 35.45320 CL ! Chloride +MASS -1 BRAD 79.90410 Br ! Bromide +MASS -1 IAD 126.90447 I ! Iodide +! Divalent ions +MASS -1 BAD 137.33000 Ba ! Barium +MASS -1 CALD 40.08000 CA ! calcium +MASS -1 MAGD 24.30000 Mg ! Magnesium +MASS -1 SRD 87.62000 Sr ! Strontium +MASS -1 ZND 65.38400 Zn ! Zinc +! Lone pairs +MASS -1 LPD 0.00000 H ! general lone pair without LJ parameters, NBFIX or NBTHOLE +MASS -1 LPDW 0.00000 H ! lone pair for water: Note overlap of SWM4 and SWM6 LPs +MASS -1 LPDO1 0.00000 H ! lone pair, amide carbonyl oxygen, based on NMA +MASS -1 LPDNA1 0.00000 H ! lone pair, general nucleic acid +MASS -1 LPR 0.00000 H ! repulsive +MASS -1 LPA1 0.00000 H ! lone pair on aromatic benz/tolu, for improving cation-pi interaction +MASS -1 LPA2 0.00000 H ! lone pair on aromatic phen/cres, for improving cation-pi interaction +MASS -1 LPA3 0.00000 H ! lone pair on aromatic mind/cres, for improving cation-pi interaction +MASS -1 LP5N 0.00000 H ! lone pair on neutral 5-ring +! Rare gases, dummy atom, lone pair +MASS -1 XED 4.00260 He ! helium +MASS -1 NED 20.17970 Ne ! neon +MASS -1 DUM 0.00000 H ! dummy atom +MASS -1 DRUD 0.00000 H ! drude particle +MASS -1 DOH2 0.00000 H ! water Drude +! Halogens +MASS -1 FDA1 18.99800 F ! aliphatic flourine +MASS -1 FDA3 18.99800 F ! aliphatic fluorine +MASS -1 FDR1 18.99800 F ! aromatic fluorine, FLOB +MASS -1 CLDA1 35.45320 CL ! aliphatic chlorine +MASS -1 CLDA3 35.45320 CL ! aliphatic chlorine +MASS -1 CLDR1 35.45320 CL ! aromatic chlorine, CHLB +MASS -1 BRDA1 79.90400 BR ! aliphatic bromine +MASS -1 BRDR1 79.90400 BR ! aromatic bromine, BROB +MASS -1 IDA1 126.90447 I ! aliphate iodine, IETH +MASS -1 IDR1 126.90447 I ! aromatic iodine, IODB +!LPD can be used as the default +MASS -1 DF2 0.00000 H ! F drude +MASS -1 DCL2 0.00000 H ! CL drude +MASS -1 DCL3 0.00000 H ! CL drude +MASS -1 DBR2 0.00000 H ! BR drude +MASS -1 DI2 0.00000 H ! I drude + +DECL -CA +DECL -C +DECL -O +DECL +N +DECL +HN +DECL +CA + +!DEFA FIRS NTER LAST CTER +!reset default patches +DEFA FIRS NONE LAST NONE +AUTOGENERATE ANGLES DIHEDRALS DRUDE PATCH !note use of DRUDE and PATCH + +RESI SWM4 0.000 NOANG NODIH ! SWM4-NDP water +GROUP +ATOM OH2 ODW 0.00000 TYPE DOH2 ALPHA -0.97825258 THOLE 1.3 +ATOM OM LPDW -1.11466 +ATOM H1 HDW 0.55733 +ATOM H2 HDW 0.55733 +BOND OH2 H1 +BOND OH2 H2 +BOND OH2 OM +BOND H1 H2 ! for SHAKE +ANGLE H1 OH2 H2 +ACCEPTOR OH2 +LONEPAIR bisector OM OH2 H1 H2 distance 0.24034492 angle 0.0 dihe 0.0 +IC H1 OH2 H2 H1 0.9572 104.52 0.00 37.74 1.5139 +IC H1 OM *OH2 H2 0.9572 52.26 180.00 52.26 0.9572 +IC H2 H1 OH2 OM 1.5139 37.74 0.01 52.26 0.24034492 +PATCH FIRST NONE LAST NONE + +RESI SWM6 0.000 NOANG NODIH ! SWM6-NDP water +GROUP ! OL1 H1 +ATOM OH2 ODW6 0.2880 TYPE DOH2 ALPHA -0.88 THOLE 1.3 ! \ / +ATOM OL1 LPDW -0.1080 ! DOH2~OH2-OM +ATOM OL2 LPDW -0.1080 ! / \ +ATOM H1 HDW 0.5307 ! OL2 H2 +ATOM H2 HDW 0.5307 ! +ATOM OM LPDW -1.1334 ! +BOND OH2 H1 +BOND OH2 H2 +BOND OH2 OL1 +BOND OH2 OL2 +BOND OH2 OM +BOND H1 H2 ! for SHAKE +ANGLE H1 OH2 H2 +ACCEPTOR OH2 +LONEPAIR bisector OL1 OH2 H1 H2 distance 0.315 angle 129.451 dihe 90.0 +LONEPAIR bisector OL2 OH2 H1 H2 distance 0.315 angle 129.451 dihe 270.0 +LONEPAIR bisector OM OH2 H1 H2 distance 0.247 angle 0.000 dihe 0.0 +IC H1 OH2 H2 H1 0.9572 104.520 0.000 37.740 1.5139 +IC H2 H1 OH2 OL1 1.5139 37.740 123.054 112.888 0.3150 +IC H1 H2 OH2 OL2 1.5139 37.740 123.054 112.888 0.3150 +IC H1 OL1 *OH2 H2 0.9572 112.888 118.270 112.888 0.9572 +IC H2 OL2 *OH2 H1 0.9572 112.888 118.270 112.888 0.9572 +IC H2 H1 OH2 OM 1.5139 37.740 0.000 52.260 0.2470 +PATCH FIRST NONE LAST NONE + +!! Monovalent Ions + +RESI LIT 1.000 ! Lithium Ion +GROUP +ATOM LIT LID 1.000 ALPHA -0.032 +PATCHING FIRST NONE LAST NONE + +RESI POT 1.000 ! Potassium Ion +GROUP +ATOM POT POTD 1.000 ALPHA -0.830 +PATCHING FIRST NONE LAST NONE + +RESI SOD 1.000 ! Sodium Ion +GROUP +ATOM SOD SODD 1.000 ALPHA -0.157 +PATCHING FIRST NONE LAST NONE + +RESI RUB 1.000 ! Rubidium Ion +GROUP +ATOM RUB RBD 1.000 ALPHA -1.370 +PATCHING FIRST NONE LAST NONE + +RESI CES 1.000 ! Caesium Ion +GROUP +ATOM CES CSD 1.000 ALPHA -2.360 +PATCHING FIRST NONE LAST NONE + +RESI F -1.000 ! Fluoride Ion +GROUP +ATOM F FAD -1.000 ALPHA -1.786 +PATCHING FIRST NONE LAST NONE + +RESI CLA -1.000 ! Chloride Ion +GROUP +ATOM CLA CLAD -1.000 ALPHA -3.969 +PATCHING FIRST NONE LAST NONE + +RESI BR -1.000 ! Bromide Ion +GROUP +ATOM BR BRAD -1.000 ALPHA -5.262 +PATCHING FIRST NONE LAST NONE + +RESI I -1.000 ! Iodide Ion +GROUP +ATOM I IAD -1.000 ALPHA -7.439 +PATCHING FIRST NONE LAST NONE + +!! Divalent Ions +! Yu et al. JCTC 2010, 6, 774-786 +RESI ZN 2.000 ! Zinc Ion +GROUP +ATOM ZN ZND 2.000 ALPHA -0.420 +PATCHING FIRST NONE LAST NONE +! +RESI MG 2.000 ! Magnesium Ion +GROUP +ATOM MG MAGD 2.000 ALPHA -0.075 +PATCHING FIRST NONE LAST NONE +! +RESI CAL 2.000 ! Calcium Ion +GROUP +ATOM CAL CALD 2.000 ALPHA -0.490 +PATCHING FIRST NONE LAST NONE +! +RESI SR 2.000 ! Strontium Ion +GROUP +ATOM SR SRD 2.000 ALPHA -0.870 +PATCHING FIRST NONE LAST NONE +! +RESI BA 2.000 ! Barium Ion +GROUP +ATOM BA BAD 2.000 ALPHA -1.560 +PATCHING FIRST NONE LAST NONE +! + +!! Dummy atom and rare gases +RESI DUM 0.000 ! DUMMY ATOM +GROUP +ATOM DUM DUM 0.000 +PATCHING FIRST NONE LAST NONE + +RESI HE 0.000 ! helium +GROUP +ATOM HE XED 0.000 ALPHA -0.205 +PATCHING FIRST NONE LAST NONE + +RESI NE 0.000 ! neon +GROUP +ATOM NE NED 0.000 ALPHA -0.396 +PATCHING FIRST NONE LAST NONE + +RESI HE1 0.000 ! helium +GROUP +ATOM HE01 XED 0.000 ALPHA -0.205 +PATCHING FIRST NONE LAST NONE + +RESI NE1 0.000 ! neon +GROUP +ATOM NE01 NED 0.000 ALPHA -0.396 +PATCHING FIRST NONE LAST NONE + +RESI ALAD 0.000 ! Alanine dipeptide +! +! HY1 OY O HT1 +! \ || HN HA || HNT / +! \ || | | || | / +! HY2--CAY--CY---N---CA--C----NT---CAT--HT2 +! / | \ +! / HB1--CB--HB3 \ +! HY3 | HT3 +! HB2 +! +GROUP +ATOM CAY CD33C -0.102 ALPHA -1.894 THOLE 2.122 +ATOM HY1 HDA3A 0.048 +ATOM HY2 HDA3A 0.048 +ATOM HY3 HDA3A 0.048 +ATOM CY CD2O1A 0.496 ALPHA -0.619 THOLE 0.295 +ATOM OY OD2C1A 0.000 ALPHA -0.579 THOLE 0.310 +ATOM LPY1 LPDO1 -0.311 +ATOM LPY2 LPDO1 -0.227 +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.250 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM CB CD33A -0.099 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA3A 0.033 +ATOM HB2 HDA3A 0.033 +ATOM HB3 HDA3A 0.033 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.295 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.310 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +ATOM NT ND2A2 -0.406 ALPHA -1.858 THOLE 0.250 +ATOM HNT HDP1A 0.296 +ATOM CAT CD33C -0.055 ALPHA -1.639 THOLE 2.122 +ATOM HTC1 HDA3A 0.055 +ATOM HTC2 HDA3A 0.055 +ATOM HTC3 HDA3A 0.055 + +BOND CAY CY CY N N CA +BOND CA C C NT NT CAT +BOND CY OY C O +BOND N HN NT HNT +BOND CA HA CA CB CB HB1 CB HB2 CB HB3 +BOND CAY HY1 CAY HY2 CAY HY3 +BOND CAT HTC1 CAT HTC2 CAT HTC3 +BOND OY LPY1 OY LPY2 +BOND O LPOA O LPOB + +IMPR CY CAY N OY N CY CA HN +IMPR C CA NT O NT C CAT HNT + +!2D correction surface +CMAP CY N CA C N CA C NT + +LONEPAIR relative LPY1 OY CY CAY distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPY2 OY CY CAY distance 0.30 angle 91.0 dihe 180.0 +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OY CY LPY1 LPY2 A11 0.82322 A22 1.14332 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +IC CY N CA C 0.00 0.00 -86.00 0.00 0.00 !phi C7eq=-86,C7ax=76 +IC N CA C NT 0.00 0.00 79.00 0.00 0.00 !psi C7eq= 79,C7ax=-55 +IC CAY CY N CA 0.00 0.00 180.00 0.00 0.00 !omega left +IC CA C NT CAT 0.00 0.00 180.00 0.00 0.00 !omega right +IC N CAY *CY OY 0.00 0.00 144.00 0.00 0.00 +IC CA CY *N HN 0.00 0.00 180.00 0.00 0.00 +IC NT CA *C O 0.00 0.00 120.00 0.00 0.00 +IC CAT C *NT HNT 0.00 0.00 180.00 0.00 0.00 +IC C N *CA CB 0.00 0.00 -120.00 0.00 0.00 !define L sugar +IC C N *CA HA 0.00 0.00 120.00 0.00 0.00 ! +IC N CA CB HB1 0.00 0.00 180.00 0.00 0.00 +IC HB1 CA *CB HB2 0.00 0.00 120.00 0.00 0.00 +IC HB1 CA *CB HB3 0.00 0.00 -120.00 0.00 0.00 +IC N CY CAY HY1 0.00 0.00 180.00 0.00 0.00 +IC HY1 CY *CAY HY2 0.00 0.00 120.00 0.00 0.00 +IC HY1 CY *CAY HY3 0.00 0.00 -120.00 0.00 0.00 +IC C NT CAT HTC1 0.00 0.00 180.00 0.00 0.00 +IC HTC1 NT *CAT HTC2 0.00 0.00 120.00 0.00 0.00 +IC HTC1 NT *CAT HTC3 0.00 0.00 -120.00 0.00 0.00 +patch first none last none + +RESI ALA 0.000 ! alanine +! +! | +! HN-N +! | HB1 +! | / +! HA-CA--CB-HB2 +! | \ +! | HB3 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD33A -0.099 ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA3A 0.033 +ATOM HB2 HDA3A 0.033 +ATOM HB3 HDA3A 0.033 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 CB HB3 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 +IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 !phi, -60. for a-helix +IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 !psi, -45. for a-helix +IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 +IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 +IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 +IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 +IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 +IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 +IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 + +RESI ARG 1.000 ! arginine +! +! | HH11 +! HN-N | +! | HB1 HG1 HD1 HE NH1-HH12 +! | | | | | //(+) +! HA-CA--CB--CG--CD--NE--CZ +! | | | | \ +! | HB2 HG2 HD2 NH2-HH22 +! O=C | +! | HH21 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP ! +ATOM CB CD32A -0.066 ALPHA -1.495 THOLE 0.947 ! CB arg ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32A -0.156 ALPHA -1.288 THOLE 0.928 ! CG arg ALPHA -1.660 THOLE 1.3 +ATOM HG1 HDA2A 0.078 +ATOM HG2 HDA2A 0.078 +GROUP +ATOM CD CD32A 0.241 ALPHA -1.700 THOLE 0.570 ! ALPHA -1.788 THOLE 0.342 +ATOM HD1 HDA2A 0.068 +ATOM HD2 HDA2A 0.068 +ATOM NE ND2P1A -0.730 ALPHA -1.320 THOLE 0.630 ! ALPHA -1.550 THOLE 1.538 +ATOM HE HDP1B 0.404 +ATOM CZ CD2N1A 1.067 ALPHA -1.418 THOLE 0.849 ! ALPHA -1.096 THOLE 0.262 +ATOM NH1 ND2P1A -0.809 ALPHA -1.023 THOLE 0.886 ! ALPHA -1.403 THOLE 1.538 +ATOM HH11 HDP1B 0.375 +ATOM HH12 HDP1B 0.375 +ATOM NH2 ND2P1A -0.809 ALPHA -1.023 THOLE 0.886 ! ALPHA -1.403 THOLE 1.538 +ATOM HH21 HDP1B 0.375 +ATOM HH22 HDP1B 0.375 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD HD1 CD HD2 +BOND CD NE NE HE NE CZ +BOND CZ NH1 NH1 HH11 NH1 HH12 +BOND CZ NH2 NH2 HH21 NH2 HH22 +BOND O LPOA O LPOB + +IMPR CZ NH1 NH2 NE +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HE NE +DONOR HH11 NH1 +DONOR HH12 NH1 +DONOR HH21 NH2 +DONOR HH22 NH2 +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 +IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 +IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 +IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 +IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 +IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 +IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 +IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 +IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 +IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 +IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 +IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 +IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 +IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 +IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 +IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 +IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 +IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 +IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 +IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 +IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 +IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 +IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 +IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 + +RESI ASN 0.000 ! asparagine +! +! | +! HN-N +! | HB1 OD1 HD21 (cis to OD1) +! | | || / +! HA-CA--CB--CG--ND2 +! | | \ +! | HB2 HD22 (trans to OD1) +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32C -0.302 ALPHA -0.948 THOLE 0.338 ! CB asn ALPHA -1.417 THOLE 1.130 +ATOM HB1 HDA2A 0.082 +ATOM HB2 HDA2A 0.082 +ATOM CG CD2O1A 0.906 ALPHA -1.583 THOLE 1.095 +ATOM OD1 OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM ND2 ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HD21 HDP1A 0.303 +ATOM HD22 HDP1A 0.351 +ATOM LPDA LPD -0.411 +ATOM LPDB LPD -0.264 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG OD1 +BOND CG ND2 ND2 HD21 ND2 HD22 +BOND O LPOA O LPOB +BOND OD1 LPDA OD1 LPDB + +IMPR CG CB ND2 OD1 ND2 HD21 HD22 CG +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LPDA OD1 CG CB distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPDB OD1 CG CB distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OD1 CG LPDA LPDB A11 0.88 A22 1.32 + +DONOR HN N +DONOR HD21 ND2 +DONOR HD22 ND2 +ACCEPTOR OD1 CG +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 +IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 +IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 +IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 +IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 +IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 +IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 +IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 +IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 +IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 +IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 +IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 +IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 +IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 + +RESI ASP -1.000 ! aspartate +! +! | +! HN-N +! | HB1 OD1 +! | | // +! HA-CA--CB--CG +! | | \ +! | HB2 OD2(-) +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.246 ALPHA -1.401 THOLE 0.880 ! CB asp ALPHA -2.528 THOLE 1.414 +ATOM HB1 HDA2A 0.007 +ATOM HB2 HDA2A 0.007 +ATOM CG CD2O2A 0.758 ALPHA -1.016 THOLE 0.899 +ATOM OD1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OD2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LP1A LPD -0.383 +ATOM LP1B LPD -0.383 +ATOM LP2A LPD -0.383 +ATOM LP2B LPD -0.383 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG OD1 CG OD2 +BOND O LPOA O LPOB +BOND OD1 LP1A OD1 LP1B +BOND OD2 LP2A OD2 LP2B + +IMPR OD1 CB OD2 CG +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LP1A OD1 CG CB distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP1B OD1 CG CB distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2A OD2 CG CB distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP2B OD2 CG CB distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OD1 CG LP1A LP1B A11 0.7229 A22 1.265 +ANISOTROPY OD2 CG LP2A LP2B A11 0.7229 A22 1.265 + +DONOR HN N +ACCEPTOR OD1 CG +ACCEPTOR OD2 CG +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 +IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 +IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 +IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 +IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 +IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 +IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 +IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 +IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 +IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 +IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 +IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 + +RESI CYS 0.000 ! cystiene +! +! | +! HN-N +! | HB1 +! | | +! HA-CA--CB--SG +! | | \ +! | HB2 HG1 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A 0.106 ALPHA -1.638 THOLE 1.256 ! CB cys ALPHA -1.273 THOLE 0.716 +ATOM HB1 HDA2A 0.013 +ATOM HB2 HDA2A 0.013 +ATOM SG SD31B 0.050 ALPHA -2.180 THOLE 1.612 +ATOM HG1 HDP1A 0.148 +ATOM LPGA LPD -0.165 +ATOM LPGB LPD -0.165 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB SG SG HG1 +BOND SG LPGA SG LPGB +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +LONEPAIR relative LPGA SG CB HG1 distance 0.75 angle 95.0 dihe 100.0 +LONEPAIR relative LPGB SG CB HG1 distance 0.75 angle 95.0 dihe 260.0 +ANISOTROPY SG CB LPGA LPGB A11 0.8800 A22 1.3200 + +DONOR HN N +DONOR HG1 SG +ACCEPTOR SG +ACCEPTOR O C +!C22 IC table +IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 +IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 +IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 +IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 +IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 +IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 +IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 +IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 +IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 +IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 +IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 + +RESI GLN 0.000 ! glutamine +! +! | +! HN-N +! | HB1 HG1 OE1 HE21 (cis to OE1) +! | | | || / +! HA-CA--CB--CG--CD--NE2 +! | | | \ +! | HB2 HG2 HE22 (trans to OE1) +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.042 THOLE 0.490 ! CB gln ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32C -0.302 ALPHA -1.583 THOLE 0.668 ! CG gln ALPHA -1.417 THOLE 1.130 +ATOM HG1 HDA2A 0.082 +ATOM HG2 HDA2A 0.082 +ATOM CD CD2O1A 0.906 ALPHA -1.583 THOLE 1.095 +ATOM OE1 OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM NE2 ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HE21 HDP1A 0.303 +ATOM HE22 HDP1A 0.351 +ATOM LPEA LPD -0.411 +ATOM LPEB LPD -0.264 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD OE1 +BOND CD NE2 NE2 HE21 NE2 HE22 +BOND O LPOA O LPOB +BOND OE1 LPEA OE1 LPEB + +IMPR CD CG NE2 OE1 NE2 HE21 HE22 CD +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LPEA OE1 CD CG distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPEB OE1 CD CG distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OE1 CD LPEA LPEB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HE21 NE2 +DONOR HE22 NE2 +ACCEPTOR OE1 CD +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 +IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 +IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 +IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 +IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 +IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 +IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 +IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 +IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 +IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 +IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 +IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 +IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 +IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 +IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 +IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 +IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 + +RESI GLU -1.000 ! glutamate +! +! | +! HN-N +! | HB1 HG1 OE1 +! | | | // +! HA-CA--CB--CG--CD +! | | | \ +! | HB2 HG2 OE2(-) +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32B -0.066 ALPHA -1.519 THOLE 1.099 ! CB glu ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32A -0.246 ALPHA -1.490 THOLE 1.088 ! CG glu ALPHA -2.528 THOLE 1.414 +ATOM HG1 HDA2A 0.007 +ATOM HG2 HDA2A 0.007 +ATOM CD CD2O2A 0.758 ALPHA -1.016 THOLE 0.899 +ATOM OE1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OE2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LP1A LPD -0.383 +ATOM LP1B LPD -0.383 +ATOM LP2A LPD -0.383 +ATOM LP2B LPD -0.383 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD OE1 CD OE2 +BOND O LPOA O LPOB +BOND OE1 LP1A OE1 LP1B +BOND OE2 LP2A OE2 LP2B + +IMPR OE1 CG OE2 CD +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LP1A OE1 CD CG distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP1B OE1 CD CG distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LP2A OE2 CD CG distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LP2B OE2 CD CG distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OE1 CD LP1A LP1B A11 0.7229 A22 1.265 +ANISOTROPY OE2 CD LP2A LP2B A11 0.7229 A22 1.265 + +DONOR HN N +ACCEPTOR OE1 CD +ACCEPTOR OE2 CD +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 +IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 +IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 +IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 +IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 +IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 +IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 +IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 +IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 +IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 +IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 +IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 +IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 +IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 +IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 + +RESI GLY 0.000 ! glycine +! +! | +! N-H +! | +! | +! HA1-CA-HA2 +! | +! | +! C=O +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD32C 0.186 ALPHA -1.066 THOLE 1.141 +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O1A 0.496 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 + +BOND N CA CA C C +N +BOND N HN C O +BOND CA HA1 CA HA2 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 +IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 +IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 +IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 +IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 +IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 +IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 +PATCHING FIRS GNTE + +RESI HSD 0.000 ! neutral HIS, proton on ND1 +! +! | HD1 HE1 +! HN-N | / +! | HB1 ND1--CE1 +! | | / || +! HA-CA--CB--CG LP || +! | | \\ || +! | HB2 CD2--NE2 +! O=C | +! | HD2 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP ! from 4MIM +ATOM CB CD32A -0.019 ALPHA -1.486 THOLE 0.427 ! CB hsd ALPHA -1.739 THOLE 0.399 +ATOM HB1 HDA2A 0.075 +ATOM HB2 HDA2A 0.075 +ATOM ND1 ND2R5A -0.057 ALPHA -1.522 THOLE 1.114 +ATOM HD1 HDP1A 0.252 +ATOM CG CD2R5A -0.250 ALPHA -1.272 THOLE 1.190 +ATOM CE1 CD2R5B 0.034 ALPHA -1.493 THOLE 1.297 +ATOM HE1 HDR5B 0.104 +ATOM NE2 ND2R5B 0.000 ALPHA -1.146 THOLE 0.816 +ATOM LPE2 LPD -0.332 +ATOM CD2 CD2R5A 0.005 ALPHA -1.515 THOLE 1.190 +ATOM HD2 HDR5A 0.113 +ATOM LPA LP5N 0.000 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG ND1 ND1 CE1 CE1 NE2 +BOND NE2 CD2 CD2 CG +BOND ND1 HD1 CE1 HE1 CD2 HD2 +BOND O LPOA O LPOB +BOND NE2 LPE2 + +IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR bisector LPA ND1 CG CE1 distance 1.173 angle 0.0 dihe 0.0 ! fylin +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +LONEPAIR bisector LPE2 NE2 CE1 CD2 distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY NE2 LPE2 CE1 CD2 A11 0.808 A22 1.384 + +DONOR HN N +DONOR HD1 ND1 +ACCEPTOR NE2 +ACCEPTOR O C +!C22 IC table +IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 +IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 +IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 +IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 +IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 +IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 +IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 +IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 +IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 +IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 +IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 +IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 +IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 +IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 +IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 +IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 +IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 + +RESI HSE 0.000 ! neutral HIS, proton on NE2, see patch HS2 below +! +! | HE1 +! HN-N / +! | HB1 ND1--CE1 +! | | / || +! HA-CA--CB--CG LP || +! | | \\ || +! | HB2 CD2--NE2 +! O=C | \ +! | HD2 HE2 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP ! from 4MIE +ATOM CB CD32A 0.015 ALPHA -1.314 THOLE 0.357 ! CB hse ALPHA -1.739 THOLE 0.399 +ATOM HB1 HDA2A 0.039 +ATOM HB2 HDA2A 0.039 +ATOM ND1 ND2R5B 0.000 ALPHA -1.522 THOLE 1.114 +ATOM LPD1 LPD -0.252 +ATOM NE2 ND2R5A -0.159 ALPHA -1.146 THOLE 0.816 +ATOM HE2 HDP1A 0.236 +ATOM CG CD2R5A -0.174 ALPHA -1.272 THOLE 1.190 +ATOM CE1 CD2R5B -0.006 ALPHA -1.493 THOLE 1.297 +ATOM HE1 HDR5B 0.145 +ATOM CD2 CD2R5A 0.027 ALPHA -1.515 THOLE 1.190 +ATOM HD2 HDR5A 0.090 +ATOM LPA LP5N 0.000 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG ND1 ND1 CE1 CE1 NE2 +BOND NE2 CD2 CD2 CG +BOND NE2 HE2 CE1 HE1 CD2 HD2 +BOND O LPOA O LPOB +BOND ND1 LPD1 + +IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR bisector LPA ND1 CG CE1 distance 1.173 angle 0.0 dihe 0.0 ! fylin +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +LONEPAIR bisector LPD1 ND1 CE1 CG distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY ND1 LPD1 CE1 CG A11 0.808 A22 1.384 + +DONOR HN N +DONOR HE2 NE2 +ACCEPTOR ND1 +ACCEPTOR O C + +!C22 IC table +IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 +IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 +IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 +IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 +IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 +IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 +IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 +IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 +IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 +IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 +IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 +IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 +IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 +IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 +IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 +IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 +IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 + +RESI HSP 1.000 ! protonated HIS +! +! | HD1 HE1 +! HN-N \ / +! | HB1 ND1--CE1 +! | | / || +! HA-CA--CB--CG || +! | | \\ || +! | HB2 CD2--NE2 +! O=C | \ +! | HD2 HE2 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +!electrostatic terms need to be refit to methylimidazolium +ATOM CB CD32A 0.017 ALPHA -0.451 THOLE 0.419 ! CB hsp ALPHA -1.739 THOLE 0.399 +ATOM HB1 HDA2A 0.078 !from HSD/HSE +ATOM HB2 HDA2A 0.078 !from HSD/HSE +ATOM ND1 ND2R5C -0.171 ALPHA -1.260 THOLE 1.194 +ATOM HD1 HDP1A 0.340 +ATOM NE2 ND2R5C -0.171 ALPHA -1.260 THOLE 1.194 +ATOM HE2 HDP1A 0.340 +ATOM CG CD2R5D -0.012 ALPHA -1.522 THOLE 1.196 +ATOM CE1 CD2R5E 0.170 ALPHA -1.500 THOLE 1.317 +ATOM HE1 HDR5E 0.170 +ATOM CD2 CD2R5D -0.012 ALPHA -1.522 THOLE 1.196 +ATOM HD2 HDR5D 0.173 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG ND1 ND1 CE1 CE1 NE2 +BOND NE2 CD2 CD2 CG +BOND ND1 HD1 CE1 HE1 CD2 HD2 NE2 HE2 +BOND O LPOA O LPOB + +!impropers need to be checked +IMPR ND1 CE1 CG HD1 NE2 CE1 CD2 HE2 +IMPR CE1 ND1 NE2 HE1 CD2 CG NE2 HD2 !CG CD2 ND1 CB is this needed: check with methylimidazolium +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HD1 ND1 +DONOR HE2 NE2 +ACCEPTOR O C + +!C22 IC table +IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 +IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 +IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 +IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 +IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 +IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 +IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 +IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 +IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 +IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 +IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 +IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 +IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 +IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 +IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 +IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 +IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 +IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 + +RESI ILE 0.000 !nomenclature of CD changed to CD1 to conform to PDB standard +! +! | HG21 HG22 +! HN-N | / +! | CG2--HG23 +! | / +! HA-CA--CB-HB HD11 +! | \ / +! | CG1--CD1--HD12 +! O=C / \ \ +! | HG11 HG12 HD13 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD31A -0.095 ALPHA -0.467 THOLE 0.399 ! CB ile ALPHA -1.302 THOLE 1.3 +ATOM HB HDA1A 0.095 +GROUP +ATOM CG2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HG21 HDA3A 0.059 +ATOM HG22 HDA3A 0.059 +ATOM HG23 HDA3A 0.059 +GROUP +ATOM CG1 CD32A -0.156 ALPHA -1.660 THOLE 1.3 +ATOM HG11 HDA2A 0.078 +ATOM HG12 HDA2A 0.078 +GROUP +ATOM CD1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HD11 HDA3A 0.059 +ATOM HD12 HDA3A 0.059 +ATOM HD13 HDA3A 0.059 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB +BOND CB CG1 CG1 HG11 CG1 HG12 +BOND CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 +BOND CG1 CD1 CD1 HD11 CD1 HD12 CD1 HD13 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 +IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 +IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 +IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 +IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 +IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 +IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 +IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 +IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 +IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 +IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 +IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 +IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 +IC CA CB CG1 CD1 1.5681 113.6300 180.0000 114.0900 1.5381 +IC CD1 CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 +IC CD1 CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 +IC CB CG1 CD1 HD11 1.5498 114.0900 -176.7800 110.3100 1.1115 +IC HD11 CG1 *CD1 HD12 1.1115 110.3100 119.7500 110.6500 1.1113 +IC HD11 CG1 *CD1 HD13 1.1115 110.3100 -119.7000 111.0200 1.1103 + +RESI LEU 0.000 ! leucine +! +! | HD11 HD12 +! HN-N | / +! | HB1 CD1--HD13 +! | | / +! HA-CA--CB--CG-HG +! | | \ +! | HB2 CD2--HD23 +! O=C | \ +! | HD21 HD22 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.636 THOLE 0.494 ! CB leu ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD31A -0.095 ALPHA -0.801 THOLE 0.660 ! CG leu ALPHA -1.302 THOLE 1.3 +ATOM HG HDA1A 0.095 +GROUP +ATOM CD1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HD11 HDA3A 0.059 +ATOM HD12 HDA3A 0.059 +ATOM HD13 HDA3A 0.059 +GROUP +ATOM CD2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HD21 HDA3A 0.059 +ATOM HD22 HDA3A 0.059 +ATOM HD23 HDA3A 0.059 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG +BOND CG CD1 CD1 HD11 CD1 HD12 CD1 HD13 +BOND CG CD2 CD2 HD21 CD2 HD22 CD2 HD23 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 +IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 +IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 +IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 +IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 +IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 +IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 +IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 +IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 +IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 +IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 +IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360 +IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168 +IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 +IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 +IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 +IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 +IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 +IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 + +RESI LYS 1.000 ! lysine +! +! | +! HN-N +! | HB1 HG1 HD1 HE1 HZ1 +! | | | | | / +! HA-CA--CB--CG--CD--CE--NZ--HZ2 +! | | | | | \ +! | HB2 HG2 HD2 HE2 HZ3 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.526 THOLE 0.544 ! CB lys ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32A -0.156 ALPHA -0.996 THOLE 0.816 ! CG lys ALPHA -1.660 THOLE 1.3 +ATOM HG1 HDA2A 0.078 +ATOM HG2 HDA2A 0.078 +GROUP +ATOM CD CD32A -0.156 ALPHA -1.458 THOLE 0.917 ! CD lys ALPHA -1.660 THOLE 1.3 +ATOM HD1 HDA2A 0.078 +ATOM HD2 HDA2A 0.078 +GROUP +ATOM CE CD32A 0.043 ALPHA -1.656 THOLE 0.895 +ATOM HE1 HDA2C 0.143 +ATOM HE2 HDA2C 0.143 +ATOM NZ ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HZ1 HDP1B 0.340 +ATOM HZ2 HDP1B 0.340 +ATOM HZ3 HDP1B 0.340 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD HD1 CD HD2 +BOND CD CE CE HE1 CE HE2 +BOND CE NZ NZ HZ1 NZ HZ2 NZ HZ3 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HZ1 NZ +DONOR HZ2 NZ +DONOR HZ3 NZ +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 +IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 +IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 +IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 +IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 +IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 +IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 +IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 +IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 +IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 +IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 +IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 +IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 +IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 +IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 +IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 +IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 +IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 +IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 +IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 +IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 +IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 + +RESI MET 0.000 ! methionine +! +! | +! HN-N +! | HB1 HG1 HE1 +! | | | | +! HA-CA--CB--CG--SD--CE--HE3 +! | | | | +! | HB2 HG2 HE2 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.066 ALPHA -1.666 THOLE 0.680 ! CB met ALPHA -1.804 THOLE 2.080 +ATOM HB1 HDA2A 0.033 +ATOM HB2 HDA2A 0.033 +GROUP +ATOM CG CD32A -0.041 ALPHA -1.300 THOLE 1.646 !ALPHA -1.460 THOLE 1.593 +ATOM HG1 HDA2A 0.082 +ATOM HG2 HDA2A 0.082 +ATOM SD SD30A 0.000 ALPHA -2.051 THOLE 1.543 +ATOM CE CD33A -0.161 ALPHA -1.587 THOLE 1.542 +ATOM HE1 HDA3A 0.082 +ATOM HE2 HDA3A 0.082 +ATOM HE3 HDA3A 0.082 +ATOM LP1A LPD -0.104 +ATOM LP1B LPD -0.104 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG SD +BOND SD CE CE HE1 CE HE2 CE HE3 +BOND O LPOA O LPOB +BOND SD LP1A SD LP1B + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR bisector LP1A SD CE CG distance 0.70 angle 95.0 dihe 100.0 +LONEPAIR bisector LP1B SD CG CE distance 0.70 angle 95.0 dihe 100.0 +ANISOTROPY SD CE LP1A LP1B A11 0.7808 A22 1.3662 + +DONOR HN N +ACCEPTOR SD +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 +IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 +IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 +IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 +IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 +IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 +IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 +IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 +IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 +IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 +IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 +IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 +IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 +IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 +IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 +IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 +IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 + +RESI PHE 0.000 ! phenylalanine +! +! | HD1 HE1 +! HN-N | | +! | HB1 CD1--CE1 +! | | // \\ +! HA-CA--CB--CG LP CZ--HZ +! | | \ __ / +! | HB2 CD2--CE2 +! O=C | | +! | HD2 HE2 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.150 ALPHA -1.361 THOLE 0.456 ! CB phe ALPHA -1.608 THOLE 0.438 +ATOM HB1 HDA2A 0.079 +ATOM HB2 HDA2A 0.079 +ATOM CG CD2R6A 0.037 ALPHA -1.550 THOLE 1.262 +ATOM CD1 CD2R6A -0.087 ALPHA -1.604 THOLE 1.262 +ATOM HD1 HDR6A 0.099 +ATOM CD2 CD2R6A -0.087 ALPHA -1.604 THOLE 1.262 +ATOM HD2 HDR6A 0.099 +ATOM CE1 CD2R6A -0.114 ALPHA -1.606 THOLE 1.262 +ATOM HE1 HDR6A 0.096 +ATOM CE2 CD2R6A -0.114 ALPHA -1.606 THOLE 1.262 +ATOM HE2 HDR6A 0.096 +ATOM CZ CD2R6A -0.133 ALPHA -1.610 THOLE 1.262 +ATOM HZ HDR6A 0.100 +ATOM LP LPA1 0.000 ! pi fylin + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG CD1 CD1 CE1 CE1 CZ +BOND CG CD2 CD2 CE2 CE2 CZ +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ HZ +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR bisector LP CG CD1 CD2 distance 1.419 angle 0.0 dihe 0.0 ! fylin +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 +IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 +IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 +IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 +IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 +IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 +IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 +IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 +IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 +IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 +IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 +IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 +IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 +IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 +IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 +IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 +IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 +IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 +IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 +IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 + +RESI PRO 0.000 ! proline +! +! +! HD1 HD2 +! | \ / +! N---CD HG1 +! | \ / +! | CG +! | / \ +! HA-CA--CB HG2 +! | / \ +! | HB1 HB2 +! O=C +! | +! +GROUP +ATOM N ND3A3 -0.203 ALPHA -1.113 THOLE 2.078 +ATOM CA CD31C -0.047 ALPHA -1.807 THOLE 0.622 +ATOM HA HDA1A 0.016 +ATOM CD CD32A -0.033 ALPHA -1.442 THOLE 0.626 +ATOM HD1 HDA2A 0.092 +ATOM HD2 HDA2A 0.092 +ATOM CB CD32A -0.115 ALPHA -1.378 THOLE 0.483 +ATOM HB1 HDA2A 0.136 +ATOM HB2 HDA2A 0.136 +ATOM CG CD32A -0.414 ALPHA -2.066 THOLE 0.644 +ATOM HG1 HDA2A 0.142 +ATOM HG2 HDA2A 0.142 +ATOM C CD2O1A 0.595 ALPHA -0.829 THOLE 1.512 +ATOM O OD2C1A 0.000 ALPHA -0.540 THOLE 1.282 +ATOM LPOA LPDO1 -0.314 +ATOM LPOB LPDO1 -0.225 + +BOND N CA CA C C +N CA HA +BOND C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG HG1 CG HG2 +BOND CG CD CD HD1 CD HD2 +BOND CD N +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA CD +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +ACCEPTOR O C +!C22 IC Table +IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 +IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 +IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 +IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 +IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 +IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 +IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 +IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 +IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 +IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 +IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 +IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 +IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 +IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 +IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 +PATCHING FIRS PROP + +RESI SER 0.000 ! serine +! +! | +! HN-N +! | HB1 +! | | +! HA-CA--CB--OG +! | | \ +! | HB2 HG1 +! O=C +! | +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.060 ALPHA -1.553 THOLE 0.421 ! CB ser ALPHA -1.000 THOLE 1.3 +ATOM HB1 HDA2A 0.080 +ATOM HB2 HDA2A 0.080 +ATOM OG OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HG1 HDP1A 0.360 +ATOM LPGA LPD -0.230 +ATOM LPGB LPD -0.230 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB OG OG HG1 +BOND O LPOA O LPOB +BOND OG LPGA OG LPGB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LPGA OG CB HG1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPGB OG CB HG1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OG CB LPGA LPGB A11 0.8108 A22 1.2162 + +DONOR HN N +DONOR HG1 OG +ACCEPTOR OG +ACCEPTOR O C +!C22 IC table +IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 +IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 +IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 +IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 +IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 +IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 +IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 +IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 +IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 +IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 +IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 + +RESI THR 0.000 ! threonine +! +! | +! HN-N +! | OG1--HG1 +! | / +! HA-CA--CB-HB +! | \ +! | CG2--HG21 +! O=C / \ +! | HG21 HG22 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD31A 0.000 ALPHA -1.655 THOLE 0.448 ! CB thr ALPHA -1.000 THOLE 1.3 +ATOM HB HDA1A 0.100 +ATOM OG1 OD31A 0.000 ALPHA -1.028 THOLE 1.3 +ATOM HG1 HDP1A 0.360 +ATOM LPGA LPD -0.230 +ATOM LPGB LPD -0.230 +GROUP +ATOM CG2 CD33A -0.180 ALPHA -1.400 THOLE 1.3 +ATOM HG21 HDA3A 0.060 +ATOM HG22 HDA3A 0.060 +ATOM HG23 HDA3A 0.060 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB +BOND CB OG1 OG1 HG1 +BOND CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 +BOND O LPOA O LPOB +BOND OG1 LPGA OG1 LPGB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LPGA OG1 CB HG1 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPGB OG1 CB HG1 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OG1 CB LPGA LPGB A11 0.8108 A22 1.2162 + +DONOR HN N +DONOR HG1 OG1 +ACCEPTOR OG1 +ACCEPTOR O C +!C22 IC table +IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 +IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 +IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 +IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 +IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 +IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 +IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 +IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 +IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 +IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 +IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 +IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 +IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 +IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 + +RESI TRP 0.000 ! tryptophan +! +! | HE3 +! HN-N | +! | HB1 CE3 +! | | / \\ +! HA-CA--CB---CG-----CD2 CZ3-HZ3 +! | | || || LP | +! | HB2 CD1 CE2 CH2-HH2 +! O=C / \ / \ // +! | HD1 NE1 CZ2 +! | | +! HE1 HZ2 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD32A -0.046 ALPHA -1.192 THOLE 0.376 ! CB trp ALPHA -2.044 THOLE 1.346 +ATOM HB1 HDA2A 0.045 +ATOM HB2 HDA2A 0.045 +ATOM CG CD2R5C -0.098 ALPHA -1.269 THOLE 1.346 +ATOM CD1 CD2R5A 0.059 ALPHA -1.612 THOLE 1.265 +ATOM HD1 HDR5A 0.083 +ATOM NE1 ND2R5A -0.276 ALPHA -1.380 THOLE 1.146 +ATOM HE1 HDP1A 0.294 +ATOM CE2 CD2R6D 0.053 ALPHA -1.267 THOLE 1.009 +ATOM CD2 CD2R6D -0.099 ALPHA -1.266 THOLE 1.344 +ATOM CE3 CD2R6A -0.034 ALPHA -1.622 THOLE 1.300 +ATOM HE3 HDR6A 0.094 +ATOM CZ3 CD2R6A -0.154 ALPHA -1.617 THOLE 1.300 +ATOM HZ3 HDR6A 0.087 +ATOM CZ2 CD2R6A -0.115 ALPHA -1.611 THOLE 1.300 +ATOM HZ2 HDR6A 0.110 +ATOM CH2 CD2R6A -0.188 ALPHA -1.621 THOLE 1.300 +ATOM HH2 HDR6A 0.140 +ATOM LP LPA3 0.000 ! pi fylin + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG CD1 CD1 NE1 NE1 CE2 +BOND CE2 CD2 CD2 CG CD2 CE3 CE3 CZ3 +BOND CZ3 CH2 CH2 CZ2 CZ2 CE2 +BOND CD1 HD1 NE1 HE1 CE3 HE3 CZ3 HZ3 +BOND CH2 HH2 CZ2 HZ2 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR bisector LP CZ2 CE2 CH2 distance 1.410 angle 0.0 dihe 0.0 ! fylin +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +DONOR HE1 NE1 +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 +IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 +IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 +IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 +IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 +IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 +IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 +IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 +IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 +IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 +IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 +IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 +IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 +IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 +IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 +IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 +IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 +IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 +IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 +IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 +IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 +IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 +IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 +IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 + +RESI TYR 0.000 ! tyrosine +! +! | HD1 HE1 +! HN-N | | +! | HB1 CD1--CE1 +! | | // \\ +! HA-CA--CB--CG LP CZ--OH +! | | \ __ / \ +! | HB2 CD2--CE2 HH +! O=C | | +! | HD2 HE2 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP ! orgi +ATOM CB CD32A -0.192 ALPHA -1.676 THOLE 0.785 ! CB tyr ALPHA -1.802 THOLE 0.148 +ATOM HB1 HDA2A 0.075 +ATOM HB2 HDA2A 0.075 +ATOM CG CD2R6A 0.086 ALPHA -1.418 THOLE 1.270 +ATOM CD1 CD2R6A -0.202 ALPHA -1.427 THOLE 1.270 +ATOM HD1 HDR6A 0.118 +ATOM CD2 CD2R6A -0.202 ALPHA -1.427 THOLE 1.270 +ATOM HD2 HDR6A 0.118 +ATOM CE1 CD2R6A -0.136 ALPHA -1.444 THOLE 1.270 +ATOM HE1 HDR6A 0.123 +ATOM CE2 CD2R6A -0.136 ALPHA -1.444 THOLE 1.270 +ATOM HE2 HDR6A 0.123 +ATOM CZ CD2R6A 0.297 ALPHA -1.174 THOLE 1.270 +ATOM OH OD31C 0.000 ALPHA -0.683 THOLE 0.601 +ATOM HH HDP1A 0.319 +ATOM LP1A LPD -0.233 +ATOM LP1B LPD -0.233 +ATOM LP LPA2 0.0000 ! pi fylin + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB1 CB HB2 +BOND CB CG CG CD1 CD1 CE1 CE1 CZ +BOND CG CD2 CD2 CE2 CE2 CZ +BOND CD1 HD1 CD2 HD2 CE1 HE1 +BOND CE2 HE2 CZ OH OH HH +BOND O LPOA O LPOB +BOND OH LP1A OH LP1B + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR bisector LP CG CD1 CD2 distance 1.421 angle 0.0 dihe 0.0 ! fylin +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 +LONEPAIR relative LP1A OH CZ HH distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LP1B OH CZ HH distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OH CZ LP1A LP1B A11 0.8108 A22 1.2162 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 +IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 +IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 +IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 +IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 +IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 +IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 +IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 +IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 +IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 +IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 +IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 +IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 +IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 +IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 +IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 +IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 +IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 +IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 +IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 +IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 + +RESI VAL 0.000 ! valine +! +! | HG11 HG12 +! HN-N | / +! | CG1--HG13 +! | / +! HA-CA--CB-HB +! | \ +! | CG2--HG21 +! O=C | \ +! | HG21 HG22 +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +GROUP +ATOM CB CD31A -0.074 ALPHA -1.210 THOLE 0.365 ! CB val ALPHA -1.914 THOLE 0.593 +ATOM HB HDA1A 0.074 +GROUP +ATOM CG1 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HG11 HDA3A 0.059 +ATOM HG12 HDA3A 0.059 +ATOM HG13 HDA3A 0.059 +GROUP +ATOM CG2 CD33A -0.177 ALPHA -2.051 THOLE 1.3 +ATOM HG21 HDA3A 0.059 +ATOM HG22 HDA3A 0.059 +ATOM HG23 HDA3A 0.059 + +BOND N CA CA C C +N CA HA +BOND N HN C O +BOND CA CB CB HB +BOND CB CG1 CG1 HG11 CG1 HG12 CG1 HG13 +BOND CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 +BOND O LPOA O LPOB + +IMPR C CA +N O N -C CA HN +CMAP -C N CA C N CA C +N + +LONEPAIR relative LPOA O C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPOB O C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY O C LPOA LPOB A11 0.82322 A22 1.14332 + +DONOR HN N +ACCEPTOR O C +!C22 IC Table +IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 +IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 +IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 +IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 +IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 +IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 +IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 +IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 +IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 +IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 +IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 +IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 +IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 +IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 +IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 +IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 + +PRES NTER 1.000 ! N-terminus in polypeptide +! +! HT1 +! (+) / +! --CA---N--HT2 +! | \ +! HA HT3 +! +DELETE ATOM HN +! +GROUP ! use in generate statement +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HT1 HDP1B 0.340 +ATOM HT2 HDP1B 0.340 +ATOM HT3 HDP1B 0.340 +ATOM CA CD31C 0.389 ALPHA -1.066 THOLE 1.141 ! charge adjusted to yield unit charge +ATOM HA HDA1C -0.017 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 + +BOND N HT1 N HT2 N HT3 + +IC C CA N HT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT1 CA *N HT3 0.0000 0.0000 -120.0000 0.0000 0.0000 + +PRES NTES 1.000 ! N-terminus in single amino acid +! Note: with CT3 use NTER +! +! HT1 +! (+) / +! --CA---N--HT2 +! | \ +! HA HT3 +! +DELETE ATOM HN +! +GROUP ! use in generate statement +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HT1 HDP1B 0.340 +ATOM HT2 HDP1B 0.340 +ATOM HT3 HDP1B 0.340 +ATOM CA CD31C 0.186 ALPHA -1.656 THOLE 0.895 ! charge adjusted to yield unit charge +ATOM HA HDA1C 0.143 ! charge adjusted to yield unit charge + +BOND N HT1 N HT2 N HT3 + +IC C CA N HT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT1 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT1 CA *N HT3 0.0000 0.0000 -120.0000 0.0000 0.0000 + +PRES GNTE 1.000 ! Glycine N-terminus (formally GLYP) in polypeptide +! +! HA1 HT1 +! |(+)/ +! --CA--N--HT2 +! | \ +! HA2 HT3 +! +DELETE ATOM HN +! +GROUP ! use in generate statement +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HT1 HDP1B 0.340 +ATOM HT2 HDP1B 0.340 +ATOM HT3 HDP1B 0.340 +ATOM CA CD32C 0.085 ALPHA -1.656 THOLE 0.895 !charge adjusted to yield neutral charge +ATOM HA1 HDA2C 0.143 +ATOM HA2 HDA2C 0.143 +ATOM C CD2O1A 0.496 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 + +BOND N HT1 N HT2 N HT3 + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES GNTS 1.000 ! Glycine N-terminus in single amino acid +! +! HA1 HT1 +! |(+)/ +! --CA--N--HT2 +! | \ +! HA2 HT3 +! +DELETE ATOM HN +! +GROUP ! use in generate statement +ATOM N ND3P3A -0.349 ALPHA -1.298 THOLE 0.895 +ATOM HT1 HDP1B 0.340 +ATOM HT2 HDP1B 0.340 +ATOM HT3 HDP1B 0.340 +ATOM CA CD32C 0.043 ALPHA -1.656 THOLE 0.895 +ATOM HA1 HDA2C 0.143 +ATOM HA2 HDA2C 0.143 + +BOND N HT1 N HT2 N HT3 + +DONOR HT1 N +DONOR HT2 N +DONOR HT3 N +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 + +!optimization required +PRES PROP 1.000 ! Proline N-Terminal !yields unit charge +! +! HA +! | +! -CA HT1 +! / \ / +! N(+) +! / \ +! -CD HT2 +! | \ +! +GROUP ! use in generate statement +ATOM N ND3P2A -0.070 ALPHA -1.479 THOLE 0.111 +ATOM HT1 HDP1B 0.266 +ATOM HT2 HDP1B 0.266 +ATOM CD CD32A 0.119 ALPHA -1.578 THOLE 1.429 +ATOM HD1 HDA2C 0.104 +ATOM HD2 HDA2C 0.104 +ATOM CA CD31C 0.114 ALPHA -1.578 THOLE 1.429 !correction from 0.165 to obtain unit charge +ATOM HA HDA1C 0.104 +ATOM C CD2O1A 0.528 ALPHA -1.342 THOLE 0.887 +ATOM O OD2C1A 0.000 ALPHA -0.682 THOLE 1.905 +ATOM LPOA LPDO1 -0.371 +ATOM LPOB LPDO1 -0.215 +ATOM CB CD32A -0.116 ALPHA -1.710 THOLE 1.295 +ATOM HB1 HDA2A 0.084 +ATOM HB2 HDA2A 0.084 +ATOM CG CD32A -0.143 ALPHA -2.049 THOLE 1.295 +ATOM HG1 HDA2A 0.071 +ATOM HG2 HDA2A 0.071 + +BOND HT1 N HT2 N + +DONOR HT1 N +DONOR HT2 N +IC HT1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES ACE 0.000 ! acetylated N-terminus in di- and polypeptides + ! use in generate statement +! +! HY1 HY2 HY3 +! \ | / +! CAY +! | +! CY=OY +! | +! +GROUP + +ATOM CAY CD33C -0.102 ALPHA -1.894 THOLE 2.122 +ATOM HY1 HDA3A 0.048 +ATOM HY2 HDA3A 0.048 +ATOM HY3 HDA3A 0.048 +ATOM CY CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM OY OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPY1 LPDO1 -0.312 +ATOM LPY2 LPDO1 -0.227 + +BOND N CY CAY CY CY OY +BOND CAY HY1 CAY HY2 CAY HY3 +BOND OY LPY1 OY LPY2 + +IMPR CY CAY N OY N CY CA HN +CMAP CY N CA C N CA C +N +CMAP CY N CA C N CA C NT !for dipeptide + +LONEPAIR relative LPY1 OY CY CAY distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPY2 OY CY CAY distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OY CY LPY1 LPY2 A11 0.82322 A22 1.14332 + +ACCEPTOR OY CY +IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 +IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 +IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 + +PRES ACP 0.000 ! acetylated N-terminus for proline + ! use in generate statement +! +!this patch is directly from ACE. It is anticipated that different electrostatic +!terms will be required for the imino proton in Proline +! +! +! HY1 HY2 HY3 +! \ | / +! CAY +! | +! CY=OY +! | +GROUP +ATOM CAY CD33C -0.102 ALPHA -1.894 THOLE 2.122 +ATOM HY1 HDA3A 0.048 +ATOM HY2 HDA3A 0.048 +ATOM HY3 HDA3A 0.048 +ATOM CY CD2O1A 0.497 ALPHA -0.675 THOLE 0.295 +ATOM OY OD2C1A 0.000 ALPHA -0.651 THOLE 0.310 +ATOM LPY1 LPDO1 -0.312 +ATOM LPY2 LPDO1 -0.227 + +BOND N CY CAY CY CY OY +BOND CAY HY1 CAY HY2 CAY HY3 +BOND OY LPY1 OY LPY2 + +IMPR CY CAY N OY N CY CA CD +CMAP CY N CA C N CA C +N +CMAP CY N CA C N CA C NT !for dipeptide + +LONEPAIR relative LPY1 OY CY CAY distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPY2 OY CY CAY distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OY CY LPY1 LPY2 A11 0.82322 A22 1.14332 + +ACCEPTOR OY CY +IC A1 A2 A3 A4 1.3474 124.31 180.00 114.26 0.9979 +IC CY N CA C 0.0000 0.00 -60.00 0.00 0.0000 +IC CY CA *N CD 0.0000 0.00 180.00 0.00 0.0000 +IC CAY CY N CA 0.0000 0.00 180.00 0.00 0.0000 +IC N CAY *CY OY 0.0000 0.00 180.00 0.00 0.0000 +IC OY CY CAY HY1 0.0000 0.00 180.00 0.00 0.0000 +IC HY1 CY *CAY HY2 0.0000 0.00 120.00 0.00 0.0000 +IC HY1 CY *CAY HY3 0.0000 0.00 -120.00 0.00 0.0000 + +!correct once neutral amine electrostatic terms are available +PRES NNEU 0.000 ! neutral N-terminus; charges from MAM1 + ! use in generate statement +! LPD1 HT1 +! : / +! --CA--N--LPX +! | \ +! HA HT2 +! +DELETE ATOM HN +GROUP +ATOM N ND3A2 0.050 ALPHA -1.450 THOLE 1.055 ! based on MAM1 +ATOM HT1 HDP1A 0.192 ! based on MAM1 +ATOM HT2 HDP1A 0.192 ! based on MAM1 +ATOM CA CD31C -0.057 ALPHA -1.066 THOLE 1.141 ! based on NTER, charge adjusted +ATOM HA HDA1A 0.094 ! based on NTER, charge adjusted +ATOM LP1D LPD -0.428 ! based on MAM1 +ATOM LPX LPD 0.000 ! based on MAM1 +ATOM C CD2O1A 0.495 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +BOND N HT1 N HT2 +BOND N LPD1 N LPX +LONEPAIR bisector LPX N HT1 HT2 distance 0.605 angle 0.0 dihe 0.0 +LONEPAIR relative LP1D N LPX CA distance 0.280 angle 105.42 dihe 180.0 +ANISOTROPY N CA HT1 HT2 A11 0.85 A22 1.05 +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES GNNU 0.000 ! neutral N-terminus for Glycine; charges from MAM1 + ! use in generate statement +! HA2 LPD1 HT1 +! \ : / +! --CA--N--LPX +! / \ +! HA1 HT2 +! +DELETE ATOM HN +GROUP +ATOM N ND3A2 0.050 ALPHA -1.450 THOLE 1.055 ! based on MAM1 +ATOM HT1 HDP1A 0.192 ! based on MAM1 +ATOM HT2 HDP1A 0.192 ! based on MAM1 +ATOM CA CD32C -0.100 ALPHA -1.066 THOLE 1.141 ! based on GNTE, charge adjusted +ATOM HA1 HDA2A 0.068 ! based on GNTE, charge adjusted +ATOM HA2 HDA2A 0.068 ! based on GNTE, charge adjusted +ATOM C CD2O1A 0.496 ALPHA -0.619 THOLE 0.317 +ATOM O OD2C1A 0.000 ALPHA -0.579 THOLE 0.370 +ATOM LPOA LPDO1 -0.311 +ATOM LPOB LPDO1 -0.227 +ATOM LPD1 LPD -0.428 ! based on MAM1 +ATOM LPX LPD 0.000 ! based on MAM1 +BOND N HT1 N HT2 +BOND N LPD1 N LPX +LONEPAIR bisector LPX N HT1 HT2 distance 0.605 angle 0.0 dihe 0.0 +LONEPAIR relative LPD1 N LPX CA distance 0.280 angle 105.42 dihe 180.0 +ANISOTROPY N CA HT1 HT2 A11 0.85 A22 1.05 +IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 + +PRES CTER -1.000 ! C-terminus for polypeptide +! +! OT2(-) +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.170 ALPHA -1.066 THOLE 1.141 +ATOM HA HDA1A -0.017 +ATOM C CD2O2A 0.483 ALPHA -1.016 THOLE 0.899 !charge adjusted to yield -1 total charge for COO atoms +ATOM OT1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OT2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LPT1 LPD -0.383 +ATOM LPT2 LPD -0.383 +ATOM LPT3 LPD -0.383 +ATOM LPT4 LPD -0.383 + +BOND C OT1 C OT2 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR C OT1 OT2 CA + +LONEPAIR relative LPT1 OT1 C OT2 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LPT3 OT2 C OT1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT4 OT2 C OT1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.7229 A22 1.265 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.7229 A22 1.265 + +IC N CA C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CTEG -1.000 ! C-terminus for polypeptide terminating with a glycine +! +! OT2(-) +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C -0.038 ALPHA -0.960 THOLE 1.078 !charge adjusted to yield -1 total charge +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O2A 0.708 ALPHA -1.016 THOLE 0.899 !charge adjusted to yield -1 total charge for COO atoms +ATOM OT1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OT2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LPT1 LPD -0.383 +ATOM LPT2 LPD -0.383 +ATOM LPT3 LPD -0.383 +ATOM LPT4 LPD -0.383 + +BOND C OT1 C OT2 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR C OT1 OT2 CA + +LONEPAIR relative LPT1 OT1 C OT2 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LPT3 OT2 C OT1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT4 OT2 C OT1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.7229 A22 1.265 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.7229 A22 1.265 + +IC N CA C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CTEP -1.000 ! C-terminus for polypeptide terminated with proline +! +! OT2(-) +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND3A3 -0.239 ALPHA -1.400 THOLE 0.754 +ATOM CA CD31C -0.141 ALPHA -1.500 THOLE 0.432 +ATOM HA HDA1A -0.014 +ATOM CD CD32A 0.017 ALPHA -1.500 THOLE 1.100 +ATOM HD1 HDA2A 0.072 +ATOM HD2 HDA2A 0.072 +ATOM CB CD32A -0.116 ALPHA -1.710 THOLE 1.295 +ATOM HB1 HDA2A 0.084 +ATOM HB2 HDA2A 0.084 +ATOM CG CD32A -0.143 ALPHA -2.049 THOLE 1.295 +ATOM HG1 HDA2A 0.071 +ATOM HG2 HDA2A 0.071 +ATOM C CD2O2A 0.708 ALPHA -1.016 THOLE 0.899 !charge adjusted to yield -1 total charge for COO atoms +ATOM OT1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OT2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LPT1 LPD -0.383 +ATOM LPT2 LPD -0.383 +ATOM LPT3 LPD -0.383 +ATOM LPT4 LPD -0.383 + +BOND C OT1 C OT2 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR C OT1 OT2 CA + +LONEPAIR relative LPT1 OT1 C OT2 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LPT3 OT2 C OT1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT4 OT2 C OT1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.7229 A22 1.265 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.7229 A22 1.265 + +IC N CA C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CTES -1.000 ! C-terminus for single amino acid +! Note: with ACE use CTER +! +! OT2(-) +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM C CD2O2A 0.526 ALPHA -1.016 THOLE 0.899 !charge adjusted to yield -1 total charge for COO atoms +ATOM OT1 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM OT2 OD2C2A 0.003 ALPHA -0.699 THOLE 2.399 +ATOM LPT1 LPD -0.383 +ATOM LPT2 LPD -0.383 +ATOM LPT3 LPD -0.383 +ATOM LPT4 LPD -0.383 + +BOND C OT1 C OT2 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR C OT1 OT2 CA + +LONEPAIR relative LPT1 OT1 C OT2 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.35 angle 110.0 dihe 180.0 +LONEPAIR relative LPT3 OT2 C OT1 distance 0.35 angle 110.0 dihe 0.0 +LONEPAIR relative LPT4 OT2 C OT1 distance 0.35 angle 110.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.7229 A22 1.265 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.7229 A22 1.265 + +IC N CA C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CNEU 0.000 ! protonated C-terminus for polypeptide +! +! OT2-HT +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND2A2 -0.406 ALPHA -1.858 THOLE 0.126 +ATOM HN HDP1A 0.296 +ATOM CA CD31C 0.103 ALPHA -1.066 THOLE 1.141 !charge adjusted from 0.858 to yield 0 total charge for COOH atoms +ATOM HA HDA1A -0.017 +ATOM C CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM OT1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OT2 OD31F 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HT HDP1A 0.374 +ATOM LPT1 LPD -0.319 +ATOM LPT2 LPD -0.319 +ATOM LPT3 LPD -0.285 +ATOM LPT4 LPD -0.285 + +BOND C OT1 C OT2 OT2 HT +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR OT1 CA OT2 C + +!standard carbonyl +LONEPAIR relative LPT1 OT1 C OT2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPT3 OT2 C HT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C HT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +IC N CA C OT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC OT1 CAN *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 !dummy IC for building dipeptides *DELETE* +IC CA C OT2 HT 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CNEG 0.000 ! protonated C-terminus for polypeptide with terminal glycine + ! Yes, the patch name is not ideal; the total charge is zero +! +! OT2-HT +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C 0.120 ALPHA -0.960 THOLE 1.078 !charge adjusted to yield 0 total charge for COOH atoms +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM OT1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OT2 OD31F 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HT HDP1A 0.374 +ATOM LPT1 LPD -0.319 +ATOM LPT2 LPD -0.319 +ATOM LPT3 LPD -0.285 +ATOM LPT4 LPD -0.285 + +BOND C OT1 C OT2 OT2 HT +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR OT1 CA OT2 C + +!standard carbonyl +LONEPAIR relative LPT1 OT1 C OT2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPT3 OT2 C HT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C HT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +IC N CA C OT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 HT 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CNES 0.000 ! protonated C-terminus for single amino acid +! Note: with ACE use CNEU +! +! OT2-HT +! / +! --C +! \\ +! OT1 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +GROUP +ATOM C CD2O3A 0.834 ALPHA -1.207 THOLE 0.708 !charge adjusted from 0.858 to yield 0 total charge for COOH atoms +ATOM OT1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OT2 OD31F 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HT HDP1A 0.374 +ATOM LPT1 LPD -0.319 +ATOM LPT2 LPD -0.319 +ATOM LPT3 LPD -0.285 +ATOM LPT4 LPD -0.285 + +BOND C OT1 C OT2 OT2 HT +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR OT1 CA OT2 C + +!standard carbonyl +LONEPAIR relative LPT1 OT1 C OT2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C OT2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPT3 OT2 C HT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C HT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +IC N CA C OT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC OT1 CA *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +!IC OT1 CAN *C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 !dummy IC for building dipeptides *DELETE* +IC CA C OT2 HT 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT1 0.000 ! methylated C-terminus from methyl acetate + ! total charge to neutralize C-terminal peptide bond + ! use in generate statement +! +! OT1 +! // +! -CA--C HT1 +! | \ / +! HA OT2--CT--HT2 +! \ +! HT3 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.059 ALPHA -0.960 THOLE 1.078 !charge adjusted to achieve neutral system +ATOM HA HDA1A -0.017 +ATOM C CD2O3A 0.697 ALPHA -1.370 THOLE 1.747 +ATOM OT1 OD2C3A 0.000 ALPHA -0.904 THOLE 0.565 +ATOM OT2 OD30C 0.000 ALPHA -0.732 THOLE 0.601 +ATOM CT CD33C -0.030 ALPHA -1.797 THOLE 0.410 +ATOM HT1 HDA3A 0.116 +ATOM HT2 HDA3A 0.116 +ATOM HT3 HDA3A 0.116 +ATOM LPT1 LPD -0.349 +ATOM LPT2 LPD -0.258 +ATOM LPT3 LPD -0.170 +ATOM LPT4 LPD -0.170 + +BOND C OT1 C OT2 OT2 CT +BOND CT HT1 CT HT2 CT HT3 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR C OT2 CA OT1 + +!LP positions and anisotropic polarizability from MAS +LONEPAIR relative LPT1 OT1 C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!LP positions and anisotropic polarizability from MAS +LONEPAIR relative LPT3 OT2 C CT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C CT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 + +PRES CT1G 0.000 ! methylated C-terminus from methyl acetate, for C-terminal GLY + ! total charge to neutralize C-terminal peptide bond + ! use in generate statement +! +! OT1 +! // +! -CA--C HT1 +! | \ / +! HA OT2--CT--HT2 +! \ +! HT3 +! +DELETE ATOM O +DELETE ATOM DO +DELETE ATOM LPOA +DELETE ATOM LPOB +! +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C 0.076 ALPHA -0.960 THOLE 1.078 !charge adjusted to achieve neutral system +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O3A 0.697 ALPHA -1.370 THOLE 1.747 +ATOM OT1 OD2C3A 0.000 ALPHA -0.904 THOLE 0.565 +ATOM OT2 OD30C 0.000 ALPHA -0.732 THOLE 0.601 +ATOM CT CD33C -0.030 ALPHA -1.797 THOLE 0.410 +ATOM HT1 HDA3A 0.116 +ATOM HT2 HDA3A 0.116 +ATOM HT3 HDA3A 0.116 +ATOM LPT1 LPD -0.349 +ATOM LPT2 LPD -0.258 +ATOM LPT3 LPD -0.170 +ATOM LPT4 LPD -0.170 + +BOND C OT1 C OT2 OT2 CT +BOND CT HT1 CT HT2 CT HT3 +BOND OT1 LPT1 OT1 LPT2 +BOND OT2 LPT3 OT2 LPT4 + +IMPR C OT2 CA OT1 + +!LP positions and anisotropic polarizability from MAS +LONEPAIR relative LPT1 OT1 C CA distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPT2 OT1 C CA distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OT1 C LPT1 LPT2 A11 0.6968 A22 1.2194 + +!LP positions and anisotropic polarizability from MAS +LONEPAIR relative LPT3 OT2 C CT distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPT4 OT2 C CT distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OT2 C LPT3 LPT4 A11 0.8108 A22 1.2162 + +ACCEPTOR OT1 C +ACCEPTOR OT2 C +IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 +IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 +IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 + +PRES CT2 0.000 ! amidated C-terminus for polypeptide +! ! use in generate statement +! | +! O=C +! | +! NT +! / \ +! HTC1 HTC2 (HTC1 is cis to O) +! +! +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD31C 0.169 ALPHA -0.960 THOLE 1.078 +ATOM HA HDA1A -0.017 +ATOM C CD2O1A 0.726 ALPHA -1.583 THOLE 1.095 !charge adjusted to yield neutral charge +ATOM O OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM NT ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HTC1 HDP1A 0.303 +ATOM HTC2 HDP1A 0.351 +ATOM LPOA LPDO1 -0.411 +ATOM LPOB LPDO1 -0.264 + +BOND C NT NT HTC1 NT HTC2 + +IMPR C CA NT O NT HTC1 HTC2 C +CMAP -C N CA C N CA C NT + +DONOR HT1 NT +DONOR HT2 NT + +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HTC1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HTC1 C *NT HTC2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT2G 0.000 ! amidated C-terminus for polypeptide terminating with a glycine +! ! use in generate statement +! | +! O=C +! | +! NT +! / \ +! HTC1 HTC2 (HTC1 is cis to O) +! +! +ATOM N ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HN HDP1A 0.272 +ATOM CA CD32C 0.090 ALPHA -0.960 THOLE 1.078 +ATOM HA1 HDA2A -0.017 +ATOM HA2 HDA2A -0.017 +ATOM C CD2O1A 0.822 ALPHA -1.583 THOLE 1.095 !charge adjusted to yield neutral charge +ATOM O OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM NT ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HTC1 HDP1A 0.303 +ATOM HTC2 HDP1A 0.351 +ATOM LPOA LPDO1 -0.411 +ATOM LPOB LPDO1 -0.264 + +BOND C NT NT HTC1 NT HTC2 + +IMPR C CA NT O NT HTC1 HTC2 C +CMAP -C N CA C N CA C NT + +DONOR HTC1 NT +DONOR HTC2 NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HTC1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HTC1 C *NT HTC2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT2S 0.000 ! amidated C-terminus for single amino acid +! ! use in generate statement +! | ! HTC1/HTC2 nomenclature to avoid conflict with NTER in single amino acids +! O=C +! | +! NT +! / \ +! HTC1 HTC2 (HTC1 is cis to O) +! +! +ATOM C CD2O1A 0.768 ALPHA -1.583 THOLE 1.095 !charge adjusted to yield neutral charge +ATOM O OD2C1A 0.035 ALPHA -0.885 THOLE 1.227 +ATOM NT ND2A1 -0.782 ALPHA -1.717 THOLE 1.132 +ATOM HTC1 HDP1A 0.303 +ATOM HTC2 HDP1A 0.351 +ATOM LPOA LPDO1 -0.411 +ATOM LPOB LPDO1 -0.264 + +BOND C NT NT HTC1 NT HTC2 + +IMPR C CA NT O NT HTC1 HTC2 C +CMAP -C N CA C N CA C NT + +DONOR HTC1 NT +DONOR HTC2 NT +IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT HTC1 0.0000 0.0000 180.0000 0.0000 0.0000 +IC HTC1 C *NT HTC2 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES CT3 0.000 ! N-Methylamide C-terminus +! ! use in generate statement +! | ! NOT compatible with PRES NTER for single amino acid due to non-unit charge +! C=O +! | +! NT-HNT +! | +! HTC1-CAT-HTC3 +! | +! HTC2 +! +ATOM NT ND2A2 -0.382 ALPHA -1.942 THOLE 0.250 +ATOM HNT HDP1A 0.272 +ATOM CAT CD33C -0.055 ALPHA -1.639 THOLE 2.122 +ATOM HTC1 HDA3A 0.055 +ATOM HTC2 HDA3A 0.055 +ATOM HTC3 HDA3A 0.055 + +BOND C NT NT HNT NT CAT +BOND CAT HTC1 CAT HTC2 CAT HTC3 + +IMPR C CA NT O NT C CAT HNT +CMAP -C N CA C N CA C NT + +DONOR HNT NT +IC N CA C NT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 +IC C NT CAT HTC1 0.0000 0.0000 60.0000 0.0000 0.0000 +IC HTC1 NT *CAT HTC2 0.0000 0.0000 120.0000 0.0000 0.0000 +IC HTC1 NT *CAT HTC3 0.0000 0.0000 -120.0000 0.0000 0.0000 + +PRES DISU 0.000 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. +! +! 2SG--2CB-- +! / +! -1CB--1SG +! +DELETE ATOM 1HG1 +DELETE ATOM 1LPGA +DELETE ATOM 1LPGB +DELETE ATOM 2HG1 +DELETE ATOM 2LPGA +DELETE ATOM 2LPGB +ATOM 1CB CD32A -0.070 ALPHA -1.888 THOLE 1.067 +ATOM 1HB1 HDA2A 0.087 +ATOM 1HB2 HDA2A 0.087 +ATOM 1SG SD30B 0.000 ALPHA -2.686 THOLE 1.082 +ATOM 1LPSA LPD -0.052 +ATOM 1LPSB LPD -0.052 +ATOM 2CB CD32A -0.070 ALPHA -1.888 THOLE 1.067 +ATOM 2HB1 HDA2A 0.087 +ATOM 2HB2 HDA2A 0.087 +ATOM 2SG SD30B 0.000 ALPHA -2.686 THOLE 1.082 +ATOM 2LPSA LPD -0.052 +ATOM 2LPSB LPD -0.052 + +BOND 1SG 2SG +BOND 1SG 1LPSA 1SG 1LPSB +BOND 2SG 2LPSA 2SG 2LPSB + +LONEPAIR bisector 1LPSA 1SG 1CB 2SG distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector 1LPSB 1SG 2SG 1CB distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector 2LPSA 2SG 2CB 1SG distance 0.90 angle 110.0 dihe 90.0 +LONEPAIR bisector 2LPSB 2SG 1SG 2CB distance 0.90 angle 110.0 dihe 90.0 +ANISOTROPY 1SG 1CB 1LPSA 1LPSB A11 0.9208 A22 1.0102 +ANISOTROPY 2SG 2CB 2LPSA 2LPSB A11 0.9208 A22 1.0102 + +IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 +IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES ASPP 0.000 ! patch for protonated aspartic acid, proton on od2 + ! via acetic acid, use in a patch statementand + ! follow with AUTOgenerate ANGLes DIHEdrals command +! +! HB1 OD1 +! | // +! -CB--CG +! | \ +! HB2 OD2-HD2 +! +DELETE ATOM LP1A +DELETE ATOM LP1B +DELETE ATOM LP2A +DELETE ATOM LP2B +! +GROUP +ATOM CB CD32C -0.208 ALPHA -2.114 THOLE 0.750 !charge adjusted +ATOM HB1 HDA2A 0.092 +ATOM HB2 HDA2A 0.092 +ATOM CG CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM OD1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OD2 OD31F 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HD2 HDP1A 0.374 +ATOM LPP1 LPD -0.319 +ATOM LPP2 LPD -0.319 +ATOM LPP3 LPD -0.285 +ATOM LPP4 LPD -0.285 + +BOND OD2 HD2 +BOND OD1 LPP1 OD1 LPP2 +BOND OD2 LPP3 OD2 LPP4 + +!standard carbonyl +LONEPAIR relative LPP1 OD1 CG OD2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPP2 OD1 CG OD2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OD1 CG LPP1 LPP2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPP3 OD2 CG HD2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPP4 OD2 CG HD2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OD2 CG LPP3 LPP4 A11 0.8108 A22 1.2162 + +DONOR HD2 OD2 +IC OD1 CG OD2 HD2 0.0000 0.0000 0.0000 0.0000 0.0000 + +PRES GLUP 0.000 ! patch for protonated glutamic acid, proton on oe2 + ! via acetic acid, use in a patch statementand + ! follow with AUTOgenerate ANGLes DIHEdrals command +! +! HG1 OE1 +! | // +! -CG--CD +! | \ +! HG2 OE2-HE2 +! +DELETE ATOM LP1A +DELETE ATOM LP1B +DELETE ATOM LP2A +DELETE ATOM LP2B +! +GROUP +ATOM CG CD32C -0.208 ALPHA -2.114 THOLE 0.750 !charge adjusted +ATOM HG1 HDA2A 0.092 +ATOM HG2 HDA2A 0.092 +ATOM CD CD2O3A 0.858 ALPHA -1.207 THOLE 0.708 +ATOM OE1 OD2C3A 0.000 ALPHA -0.922 THOLE 1.539 +ATOM OE2 OD31F 0.000 ALPHA -1.280 THOLE 1.124 +ATOM HE2 HDP1A 0.374 +ATOM LPP1 LPD -0.319 +ATOM LPP2 LPD -0.319 +ATOM LPP3 LPD -0.285 +ATOM LPP4 LPD -0.285 + +BOND OE2 HE2 +BOND OE1 LPP1 OE1 LPP2 +BOND OE2 LPP3 OE2 LPP4 + +!standard carbonyl +LONEPAIR relative LPP1 OE1 CD OE2 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPP2 OE1 CD OE2 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OE1 CD LPP1 LPP2 A11 0.6968 A22 1.2194 + +!from MeOH +LONEPAIR relative LPP3 OE2 CD HE2 distance 0.35 angle 110.9 dihe 91.0 +LONEPAIR relative LPP4 OE2 CD HE2 distance 0.35 angle 110.9 dihe 269.0 +ANISOTROPY OE2 CD LPP3 LPP4 A11 0.8108 A22 1.2162 + +DONOR HE2 OE2 +IC OE1 CD OE2 HE2 0.0000 0.0000 0.0000 0.0000 0.0000 + +!based on the optimized neutral propylamine, fylin +!!!!!!see NNEU above (?) +PRES LSN 0.000 ! patch for neutral lysine based on propylamine + ! use in a patch statement + ! follow with AUTOgenerate ANGLes DIHEdrals command +DELETE ATOM HZ3 +GROUP +ATOM CE CD32A -0.144 ALPHA -1.307 THOLE 0.855 +ATOM HE1 HDA2A 0.094 +ATOM HE2 HDA2A 0.094 +ATOM NZ ND3A2 0.050 ALPHA -1.450 THOLE 1.055 +ATOM HZ1 HDP1A 0.162 +ATOM HZ2 HDP1A 0.162 +ATOM LPD1 LPD -0.418 +ATOM LPX LPD 0.000 +BOND NZ CE NZ HZ1 NZ HZ2 NZ LPD1 NZ LPX +BOND CE HE1 CE HE2 CE CD +LONEPAIR bisector LPX NZ HZ1 HZ2 distance 0.605 angle 0.0 dihe 0.0 +LONEPAIR relative LPD1 NZ LPX CE distance 0.280 angle 105.42 dihe 180.0 +ANISOTROPY NZ CE HZ1 HZ2 A11 0.85 A22 1.05 +IC CB CG CD CE 0.00 0.00 30.0 0.00 0.00 +IC CG CD CE NZ 0.00 0.00 120.0 0.00 0.00 +IC CD CE NZ HZ1 0.00 0.00 180.0 0.00 0.00 +IC CE HZ1 *NZ HZ2 0.00 0.00 120.0 0.0 0.0 +IC HE1 CE NZ HZ1 0.00 0.00 -62.0 0.0 0.0 +IC NZ HE1 *CZ HE2 0.00 0.00 120.0 0.0 0.0 +!!NOTE: The initial position of the lonepair (LPD1) is not accurate generated by "coor shake". +!! The position will be correct once the minimization is applied. +!! ex: MINI SD nstep 0 + + + + +PRES LINK 0.000 ! linkage for cyclic peptide, may also be used for joining images + ! Note that the following number is required to include the CMAP + ! terms for the residues surrounding the link + ! 1 refers to residue 1 position from the C terminus (residue n-1) + ! 2 refers to the C terminus (residue n) which is a glycine + ! 3 refers to the N terminus (usually residue 1) + ! 4 refers to the N terminus plus 1 (usually residue 2) + ! use in a patch statement, perform initial + ! generation using first NONE last NONE + ! follow with AUTOgenerate ANGLes DIHEdrals command +BOND 2C 3N +IMPR 3N 2C 3CA 3HN 2C 2CA 3N 2O + +CMAP 1C 2N 2CA 2C 2N 2CA 2C 3N +CMAP 2C 3N 3CA 3C 3N 3CA 3C 4N + +IC 2N 2CA 2C 3N 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 3N 2CA *2C 2O 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2CA 2C 3N 3CA 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2C 3N 3CA 3C 0.0000 0.0000 180.0000 0.0000 0.0000 +IC 2C 3CA *3N 3HN 0.0000 0.0000 180.0000 0.0000 0.0000 + +PRES HS2 0.000 ! Patch for neutral His, move proton from ND1 to NE2 (convert HSD to HSE) + ! use in a patch statement ! updated based on HSE update by fylin + ! follow with AUTOgenerate ANGLes DIHEdrals command +! HE1 +! / +! HB1 ND1--CE1 +! | / | +! -CB--CG LP | +! | \ | +! HB2 CD2--NE2 +! | \ +! HD2 HE2 +! +DELETE ATOM HD1 +DELETE ATOM LPE2 +DELETE ACCE NE2 +GROUP +ATOM CB CD32A 0.015 ALPHA -1.314 THOLE 0.357 +ATOM HB1 HDA2A 0.039 +ATOM HB2 HDA2A 0.039 +ATOM ND1 ND2R5B 0.000 ALPHA -1.522 THOLE 1.114 +ATOM LPD1 LPD -0.252 +ATOM NE2 ND2R5A -0.159 ALPHA -1.146 THOLE 0.816 +ATOM HE2 HDP1A 0.236 +ATOM CG CD2R5A -0.174 ALPHA -1.272 THOLE 1.190 +ATOM CE1 CD2R5B -0.006 ALPHA -1.493 THOLE 1.297 +ATOM HE1 HDR5B 0.145 +ATOM CD2 CD2R5A 0.027 ALPHA -1.515 THOLE 1.190 +ATOM HD2 HDR5A 0.090 +ATOM LPA LP5N 0.000 + +BOND NE2 HE2 +BOND ND1 LPD1 + +IMPR NE2 CD2 CE1 HE2 + +LONEPAIR bisector LPA ND1 CG CE1 distance 1.173 angle 0.0 dihe 0.0 ! fylin +LONEPAIR bisector LPD1 ND1 CE1 CG distance 0.35 angle 179.99 dihe 179.99 +ANISOTROPY ND1 LPD1 CE1 CG A11 0.808 A22 1.384 + +DONOR HE2 NE2 +ACCEP ND1 + +IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 + + +PRES KAC 0.000 ! patch for Lys (K) acetylation, jal +DELETE ATOM HZ1 +DELETE ATOM HZ2 +DELETE ATOM HZ3 +GROUP +ATOM CE CD32C 0.150 ALPHA -1.283 THOLE 0.718 +ATOM HE1 HDA2A 0.042 +ATOM HE2 HDA2A 0.042 +ATOM NZ ND2A2 -0.580 ALPHA -1.505 THOLE 0.407 +ATOM HZ HDP1A 0.305 +GROUP +ATOM CH CD2O1A 0.791 ALPHA -1.707 THOLE 1.495 +ATOM OH OD2C1A 0.039 ALPHA -0.953 THOLE 0.910 +ATOM LPA LPDO1 -0.426 +ATOM LPB LPDO1 -0.269 +GROUP +ATOM CH3 CD33C -0.235 ALPHA -1.531 THOLE 0.363 +ATOM HH31 HDA3A 0.047 +ATOM HH32 HDA3A 0.047 +ATOM HH33 HDA3A 0.047 + +BOND NZ HZ NZ CH +BOND CH OH CH CH3 +BOND CH3 HH31 CH3 HH32 CH3 HH33 +BOND OH LPA OH LPB + +IMPR NZ CH CE HZ +IMPR CH CH3 NZ OH + +LONEPAIR relative LPA OH CH CH3 distance 0.30 angle 91.0 dihe 0.0 +LONEPAIR relative LPB OH CH CH3 distance 0.30 angle 91.0 dihe 180.0 +ANISOTROPY OH CH LPA LPB A11 0.82322 A22 1.14332 + +IC CD CE NZ CH 0.0000 0.00 180.00 0.00 0.0000 +IC CE CH *NZ HZ 0.0000 0.00 180.00 0.00 0.0000 +IC CE NZ CH CH3 0.0000 0.00 180.00 0.00 0.0000 +IC NZ CH3 *CH OH 0.0000 0.00 180.00 0.00 0.0000 +IC NZ CH CH3 HH31 0.0000 0.00 180.00 0.00 0.0000 +IC HH31 CH *CH3 HH32 0.0000 0.00 120.00 0.00 0.0000 +IC HH31 CH *CH3 HH33 0.0000 0.00 -120.00 0.00 0.0000 + +end + +read para card flex !append +* Drude polarizable FF parameters +* + +atoms +!pre 2020 nucleic acid types, temporarily in the 2023 main file +!to be removed once the update nucleic acid parameters are put to use +MASS -1 OD2C2C 15.99940 ! carboxylate O, anionic (phosphate), nucleic acids +MASS -1 OD30BN 15.99940 ! ester oxygen (phosphate), nucleic acid +MASS -1 PD1AN 30.974000 ! phosphorus, (DMP), nucleic acids +! +MASS -1 HDP1A 1.00800 ! polar H, general +MASS -1 HDP1B 1.00800 ! polar H, ammonium cations +MASS -1 HDP1C 1.00800 ! polar H, aldehyde +MASS -1 HDA1A 1.00800 ! aliphatic H, (-CH), general +MASS -1 HDA1C 1.00800 ! aliphatic H, (-CH), special case for ammonium cations +MASS -1 HDA1R5 1.00800 ! aliphatic H, (-CH), 5-membered ring +MASS -1 HDA2A 1.00800 ! aliphatic H, (-CH2), general +MASS -1 HDA2C 1.00800 ! aliphatic H, (-CH2), special case for ammonium cations +MASS -1 HDA2E 1.00800 ! aliphatic H, (-CH2), ethers +MASS -1 HDA2R5 1.00800 ! aliphatic H, (-CH2), 5-membered ring +MASS -1 HDA3A 1.00800 ! aliphatic H, (-CH3), general +MASS -1 HDA3B 1.00800 ! aliphatic H, (-CH3), special case for methanol +MASS -1 HDA3C 1.00800 ! aliphatic H, (-CH3), special case for ammonium cations +MASS -1 HDR5A 1.00800 ! 5-membered ring, HG and HD2 in imidazole +MASS -1 HDR5B 1.00800 ! 5-membered ring, HE1 in imidazole +MASS -1 HDR5C 1.00800 ! 5-membered ring, H on carbon adjacent to N in pyrrole +MASS -1 HDR5D 1.00800 ! 5-membered ring, HG and HD2 in imidazolium +MASS -1 HDR5E 1.00800 ! 5-membered ring, HE1 in imidazolium +MASS -1 HDR6A 1.00800 ! aromatic H, 6-membered ring, general +MASS -1 HDR6B 1.00800 ! aromatic H, 6-membered ring, adjacent to N (pyridine) +MASS -1 HDR6C 1.00800 ! aromatic H, 6-membered ring, between 2 N's (pyrimidine) +MASS -1 HD2C1A 1.00800 ! internal alkene H +MASS -1 HD2C1B 1.00800 ! terminal alkene H +MASS -1 HDW 1.00800 ! water H, SWM4 and SWM6 +MASS -1 CD2C1A 12.01100 ! alkene C, internal alkene C, single unsaturation +MASS -1 CD2C1B 12.01100 ! alkene C, terminal alkene C +MASS -1 CD2O1A 12.01100 ! carbonyl C, amide +MASS -1 CD2O1C 12.01100 ! carbonyl C, aldehyde +MASS -1 CD2O1D 12.01100 ! carbonyl C, ketone +MASS -1 CD2O2A 12.01100 ! carboxylate C, anionic +MASS -1 CD2O3A 12.01100 ! carbonyl C, in esters and acids (neutral) +MASS -1 CD2O4A 12.01100 ! carbonyl C, nucleic acid bases +MASS -1 CD2N1A 12.01100 ! guanidinium C +MASS -1 CD2R5A 12.01100 ! 5-membered ring, CG and CD2 in imidazole +MASS -1 CD2R5B 12.01100 ! 5-membered ring, CE1 in imidazole +MASS -1 CD2R5C 12.01100 ! 5-membered ring, pyrole, adjacent to N +MASS -1 CD2R5D 12.01100 ! 5-membered ring, CG and CD2 in imidizolium +MASS -1 CD2R5E 12.01100 ! 5-membered ring, CE1 in imidizolium +MASS -1 CD2R5F 12.01100 ! C8, nucleic acid purine bases +MASS -1 CD2R6A 12.01100 ! aromatic C, 6-membered ring +MASS -1 CD2R6B 12.01100 ! aromatic C, 6-membered ring, adjacent to N (pyridine) +MASS -1 CD2R6C 12.01100 ! aromatic C, 6-membered ring, between 2 heteroatoms (pyrimidine) +MASS -1 CD2R6D 12.01100 ! aromatic C, 6-membered ring, bridging far from N (indole) +MASS -1 CD2R6F 12.01100 ! aromatic C, 6-membered ring, bridging adjacent to N7 (purine) +MASS -1 CD2R6H 12.01100 ! C6, nucleic acid pyrmidine bases +MASS -1 CD2R6J 12.01100 ! C5, nucleic acid pyrmidine bases +MASS -1 CD2R6I 12.01100 ! aromatic C, 6-membered ring, adjacent to anionic O phenolate +MASS -1 CD30A 12.01100 ! aliphatic sp3 C, 0 H +MASS -1 CD30FA 12.01100 ! aliphatic sp3 C, 1 H, furanoses, anomeric C1 +MASS -1 CD31A 12.01100 ! aliphatic sp3 C, 1 H +MASS -1 CD31C 12.01100 ! aliphatic sp3 C, 1 H, special case for carbons adjacent to esters/amides +MASS -1 CD31DC 12.01100 ! for D-amino acids, jal +MASS -1 CD31FA 12.01100 ! aliphatic sp3 C, 1 H, furanoses, anomeric C1 +MASS -1 CD31FB 12.01100 ! aliphatic sp3 C, 1 H, furanoses, C2,C3 +MASS -1 CD31FC 12.01100 ! aliphatic sp3 C, 1 H, furanoses, C4 +MASS -1 CD31G 12.01100 ! aliphatic sp3 C, 1 H, glycerol, xhe +MASS -1 CD315A 12.01100 ! aliphatic sp3 C, 1 H, ether, 5-memberd ring, CPNM +MASS -1 CD315B 12.01100 ! aliphatic sp3 C, 1 H, ether, 5-memberd ring, TF2M +MASS -1 CD316A 12.01100 ! aliphatic sp3 C, 1 H, 6-membered ring +MASS -1 CD31HA 12.01100 ! aliphatic sp3 C, 1 H, hexopyranoses, C1 anomeric carbon, dpatel +MASS -1 CD31HB 12.01100 ! aliphatic sp3 C, 1 H, hexopyranoses, C2, C3 and C4 +MASS -1 CD31HC 12.01100 ! aliphatic sp3 C, 1 H, hexopyranoses, C5 +!======atom type added for glycopetide and modified carbohydrate======ahaile==08/08/2021 +MASS -1 CD30HA 12.01100 ! aliphatic sp3 C, 1 H, hexopyranoses +MASS -1 CD32HB 12.01100 ! aliphatic sp3 C, 1 H, hexopyranoses +MASS -1 CD32HC 12.01100 ! aliphatic sp3 C, 1 H, hexopyranoses +!====================================================================== +MASS -1 CD32A 12.01100 ! aliphatic sp3 C, 2 H +MASS -1 CD32B 12.01100 ! aliphatic sp3 C, 2 H, added for GLU and phosphoglycerol lipids, from CD32A +MASS -1 CD32C 12.01100 ! aliphatic sp3 C, 2 H, special case for carbons adjacent to esters/amides +MASS -1 CD32E 12.01100 ! aliphatic sp3 C, 2 H, ether, for CH2 adjacent to O in linear ethers +MASS -1 CD32F 12.01100 ! aliphatic sp3 C, 2 H, ethylene glycol, glycerol, xhe +MASS -1 CD325A 12.01100 ! aliphatic sp3 C, 2 H, 5-membered ring +MASS -1 CD325B 12.01100 ! aliphatic sp3 C, 2 H, ether, 5-membered ring, THF +MASS -1 CD326A 12.01100 ! aliphatic sp3 C, 2 H, 6-membered ring +MASS -1 CD326B 12.01100 ! aliphatic sp3 C, 2 H, ether, 6-membered ring, THP +MASS -1 CD33A 12.01100 ! aliphatic sp3 C, 3 H +!!MODEL unique +MASS -1 CD33B 12.01100 ! aliphatic sp3 C, 3 H, special case for methanol +!! +MASS -1 CD33C 12.01100 ! aliphatic sp3 C, 3 H, special case for C adjacent to carbonyls/estersphosphate +MASS -1 CD33E 12.01100 ! aliphatic sp3 C, 3 H, special case for CH3 adjacent to O in linear ethers + +MASS -1 ND2A1 14.00700 ! amide, primary (ACEM) +MASS -1 ND2A2 14.00700 ! amide, secondary (NMA, peptide bond) +MASS -1 ND2A3 14.00700 ! amide, tertiary (DMA) +MASS -1 ND2B1 14.00700 ! amine, primary (NA bases) +MASS -1 ND2R5A 14.00700 ! neutral his protonated ring nitrogen +MASS -1 ND2R5B 14.00700 ! neutral his unprotonated ring nitrogen +MASS -1 ND2R5C 14.00700 ! positive his protonated ring nitrogen +MASS -1 ND2R5D 14.00700 ! aromatic N, 5-membered, nucleic acid purine bases +MASS -1 ND2R5E 14.00700 ! neutral unprotonated ring nitrogen, nucleic acid purine bases +MASS -1 ND2R5F 14.00700 ! N9, nucleic acid guanine base +MASS -1 ND2R6A 14.00700 ! aromatic N, 6-membered ring (pyridine) +MASS -1 ND2R6B 14.00700 ! aromatic N, 6-membered ring (pyrimidine, N-C-N connectivity) +MASS -1 ND2R6C 14.00700 ! aromatic N, 6-membered ring: protonated: nucleic acid pyrimidine bases +MASS -1 ND2R6D 14.00700 ! N1, nucleic acid thymine base +MASS -1 ND2P1A 14.00700 ! protonated sp2 nitrogen: guanidinium +MASS -1 ND3P2A 14.00700 ! protonated sp3 nitrogen, 0, 1 or 2 Hs +MASS -1 ND3P3A 14.00700 ! protonated sp3 nitrogen, 3 or 4 Hs (includes ammonia) +MASS -1 ND3A2 14.00700 ! neutral aliphatic amines +MASS -1 ND3A3 14.00700 ! imino nitrogen, proline + +MASS -1 OD2C1A 15.99940 ! carbonyl O, amides +MASS -1 OD2C1B 15.99940 ! carbonyl O, NA bases +MASS -1 OD2C1C 15.99940 ! carbonyl O, aldehyde +MASS -1 OD2C1D 15.99940 ! carbonyl O, ketone +MASS -1 OD2C2A 15.99940 ! carboxylate O, anionic (acetate) +MASS -1 OD2C2B 15.99940 ! carboxylate O, anionic (phosphate), lipids +MASS -1 OD2C3A 15.99940 ! carbonyl O, neutral (esters) +MASS -1 OD30A 15.99940 ! ether oxygen +MASS -1 OD30B 15.99940 ! ester oxygen (phosphate), lipid & nucleic acids +MASS -1 OD30BR 15.99940 ! ester oxygen (phosphate), RNA specific +MASS -1 OD30C 15.99940 ! ester oxygen (esters) +MASS -1 OD30D 15.99940 ! ester oxygen (terminal phosphate), MP_1 +MASS -1 OD30E 15.99940 ! ionized hydroxyl oxygen, PHET (phenolate) +MASS -1 OD305A 15.99940 ! ether oxygen, 5-membered ring (tetrahydrofuran) +MASS -1 OD306A 15.99940 ! ether oxygen, 6-membered ring (tetrahydropyran) +MASS -1 OD31A 15.99940 ! hydroxyl oxygen +MASS -1 OD31B 15.99940 ! hydroxyl oxygen, special case for long, primary alcohols +MASS -1 OD31C 15.99940 ! hydroxyl oxygen, phenol +MASS -1 OD31D 15.99940 ! hydroxyl oxygen, methylphosphate +MASS -1 OD31E 15.99940 ! hydroxyl oxygen, ethylene glycol, glycerol, xhe +MASS -1 OD31F 15.99940 ! hydroxyl oxygen, acids +MASS -1 OD31G 15.99940 ! hydroxyl oxygen, to resolve DNA/RNA 3TER conflict, jal +MASS -1 ODW 15.99940 ! water oxygen, SWM4 +MASS -1 ODW6 15.99940 ! water oxygen, SWM6 +! phosphorous +MASS -1 PD1A 30.974000 ! phosphorus, (DMP), lipids +! Sulfurs +MASS -1 SD1A 32.06000 ! sulfate ion, based on PD1A, a&a +MASS -1 SD31A 32.06000 ! MESH +MASS -1 SD31B 32.06000 ! ETSH +MASS -1 SD30A 32.06000 ! EMS, DMS +MASS -1 SD30B 32.06000 ! DMDS +MASS -1 SD2C2A 32.06000 ! MES, thiolates +MASS -1 SD2C2B 32.06000 ! ETS, thiolates + +! Monovalent ions +MASS -1 LID 6.94120 ! Lithium +MASS -1 POTD 39.10200 ! Potassium +MASS -1 SODD 23.00000 ! Sodium +MASS -1 RBD 85.46783 ! Rubidium +MASS -1 CSD 132.90545 ! Caesium +MASS -1 FAD 18.99840 ! Fluoride +MASS -1 CLAD 35.45320 ! Chloride +MASS -1 BRAD 79.90410 ! Bromide +MASS -1 IAD 126.90447 ! Iodide +! Divalent ions +MASS -1 BAD 137.33000 ! Barium +MASS -1 CALD 40.08000 ! calcium +MASS -1 MAGD 24.30000 ! Magnesium +MASS -1 SRD 87.62000 ! Strontium +MASS -1 ZND 65.38400 ! Zinc +! Lone pairs +MASS -1 LPD 0.00000 ! general lone pair without LJ parameters, NBFIX or NBTHOLE +MASS -1 LPDW 0.00000 ! lone pair for water: Note overlap of SWM4 and SWM6 LPs +MASS -1 LPDO1 0.00000 ! lone pair, amide carbonyl oxygen, based on NMA +MASS -1 LPDNA1 0.00000 ! lone pair, general nucleic acid +MASS -1 LPR 0.00000 ! repulsive +MASS -1 LPA1 0.00000 ! lone pair on aromatic benz/tolu, for improving cation-pi interaction +MASS -1 LPA2 0.00000 ! lone pair on aromatic phen/cres, for improving cation-pi interaction +MASS -1 LPA3 0.00000 ! lone pair on aromatic mind/cres, for improving cation-pi interaction +MASS -1 LP5N 0.00000 ! lone pair on neutral 5-ring +! Rare gases, dummy atom, lone pair +MASS -1 XED 4.00260 ! helium +MASS -1 NED 20.17970 ! neon +MASS -1 DUM 0.00000 ! dummy atom +MASS -1 DRUD 0.00000 ! drude particle +MASS -1 DOH2 0.00000 ! water Drude +! Halogens +MASS -1 FDA1 18.99800 ! aliphatic flourine +MASS -1 FDA3 18.99800 ! aliphatic fluorine +MASS -1 FDR1 18.99800 ! aromatic fluorine, FLOB +MASS -1 CLDA1 35.45320 ! aliphatic chlorine +MASS -1 CLDA3 35.45320 ! aliphatic chlorine +MASS -1 CLDR1 35.45320 ! aromatic chlorine, CHLB +MASS -1 BRDA1 79.90400 ! aliphatic bromine +MASS -1 BRDR1 79.90400 ! aromatic bromine, BROB +MASS -1 IDA1 126.90447 ! aliphate iodine, IETH +MASS -1 IDR1 126.90447 ! aromatic iodine, IODB +!LPD can be used as the default +MASS -1 DF2 0.00000 ! F drude +MASS -1 DCL2 0.00000 ! CL drude +MASS -1 DCL3 0.00000 ! CL drude +MASS -1 DBR2 0.00000 ! BR drude +MASS -1 DI2 0.00000 ! I drude + +BONDS +!atom type Kb b0 +!============================================ +! +ND2A1 CD2O1A 420.00 1.350 ! ACEM, acetamide +ND2A1 CD2R6B 360.00 1.362 ! CTY, va +ND2A1 CD2R6C 360.00 1.369 ! ADE, cmb +ND2A1 HDP1A 480.00 1.025 ! ACEM, acetamide +ND2A2 CD2O1A 376.20 1.285 ! NMA, N-methylacetamide %PEML jan13 +ND2A2 CD31C 307.90 1.445 ! ALAD, alanine dipeptide %PEML jan13 +ND2A2 CD32C 338.00 1.425 ! GLYD, glycine dipeptide %PEML jan13 +ND2A2 CD33C 330.80 1.461 ! NMA, N-methylacetamide %PEML jan13 +ND2A2 HDP1A 459.30 1.030 ! NMA, N-methylacetamide %PEML jan13 +ND2A2 HDP1B 459.30 1.030 ! NMA, N-methylacetamide %PEML jan13 +ND2A3 CD2O1A 370.00 1.310 ! DMA, N,N-dimethylacetamide +ND2A3 CD33C 330.00 1.450 ! DMA, N,N-dimethylacetamide +ND3A2 LPD 0.00 0.000 ! mam1, eam1, pam1, fylin +ND3A2 HDP1A 520.00 1.014 ! mam1 , fylin +ND3A2 CD33A 380.00 1.450 ! mam1 , fylin +ND3A2 CD32A 390.00 1.465 ! eam1 , fylin +ND3A2 CD31C 390.00 1.465 ! NNEU, based on ND3A2 CD32A from eam1 +ND3A2 CD32C 390.00 1.465 ! NNEU-Gly, based on ND3A2 CD32A from eam1 +ND3A3 HDP1A 440.00 1.025 ! PRLD, pyrrolidine, PEML % CHECK THESE ?? +ND2B1 CD2R6B 360.00 1.362 ! NA bases, cmb 04/10 +ND2B1 CD2R6C 360.00 1.369 ! NA bases, cmb 04/10 +ND2B1 HDP1A 480.00 1.025 ! NA bases, cmb 04/10 +ND2P1A CD2N1A 463.00 1.400 ! GUAN, geo opt (EH) +ND2P1A CD32A 285.30 1.488 ! GUAN, from GEOM OPT (PEML) +ND2P1A CD33A 285.30 1.488 ! GUAN, from GEOM OPT (PEML) +ND2P1A HDP1B 455.00 1.010 ! GUAN, geo opt (EH) +ND2R5A CD2R5A 400.00 1.380 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5A CD2R5B 400.00 1.360 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5A CD2R6D 279.90 1.415 ! INDO, indole +ND2R5A CD2R6F 428.02 1.381 ! PUR0/1, purine +ND2R5A HDP1A 466.00 1.000 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5B CD2R5A 400.00 1.380 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5B CD2R5B 400.00 1.320 ! IMID, imidazole, geom + freq, peml 2006 +ND2R5B CD2R5F 400.00 1.320 ! IMID, imidazole, geom + freq, peml 2006, jal +ND2R5B CD2R6F 428.02 1.381 ! PUR0/1, purine +ND2R5C CD2R5D 400.00 1.375 ! IMIM, geo opt (EH) +ND2R5C CD2R5E 400.00 1.350 ! IMIM, geo opt (EH) +ND2R5C HDP1A 466.00 1.000 ! IMIM, first guess (EH) +ND2R5D CD2R5F 400.00 1.370 ! ADE, jal +ND2R5D CD2R6F 350.00 1.370 ! ADE, cmb 04/10 +ND2R5D CD32A 400.00 1.456 ! Et-Gua, cmb 04/10 +ND2R5D CD33A 400.00 1.456 ! ADE, cmb 04/10 +ND2R5D HDP1A 466.00 1.000 ! ADE, IMID, imidazole, geom + freq, peml 2006 +ND2R5E CD2R5F 400.00 1.320 ! GUA/ADE, jal +ND2R5E CD2R6F 428.02 1.381 ! GUA/ADE, cmb 04/10 +ND2R6A CD2R6B 407.80 1.334 ! PYR, pyridine, geom + freq, peml 2005 +ND2R6B CD2O4A 360.00 1.330 ! CYT, va, jal +ND2R6B CD2R6B 350.10 1.312 ! PYRM, pyrimidine, geom + freq, peml 2006 +ND2R6B CD2R6C 423.40 1.322 ! PYRM, pyrimidine, geom + freq, peml 2006 +ND2R6B CD2R6F 420.00 1.332 ! PUR0/1, purine +ND2R6B CD2R6H 420.00 1.332 ! CYT, cmb 04/10 +ND2R6B HDP1A 474.00 1.010 ! CYT +ND2R6C CD33A 400.00 1.456 ! CYT, cmb 04/10 +ND2R6C CD2O4A 340.00 1.370 ! THY, va, jal +ND2R6C CD2R6C 400.00 1.392 ! GUA, cmb 04/10 +ND2R6C CD2R6H 420.00 1.332 ! CYT, cmb 04/10 +ND2R6C HDP1A 474.00 1.023 ! THY, cmb 04/10 +ND3A3 CD2O1A 479.10 1.364 ! 450.00 1.340 ! PRO +ND3A3 CD31C 233.52 1.437 ! 180.70 1.510 ! PRO +ND3A3 CD32A 215.01 1.461 ! 180.70 1.510 ! PRO +ND3A3 CD32C 180.70 1.510 ! PRLD, pyrrolidine, PEML +ND3P2A CD31A 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P2A CD31C 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P2A CD32A 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P2A CD33A 215.00 1.510 ! NC4, qm, EH 2007, ammonium cations +ND3P3A CD31A 180.70 1.510 ! NTER, NC1, qm, EH 2007, From ND3P3A CD33A %% +ND3P3A CD31C 180.70 1.510 ! NTER, NC1, qm, EH 2007, From ND3P3A CD33A %% +ND3P3A CD32A 215.00 1.510 ! NC1, qm, EH 2007, ammonium cations +ND3P3A CD32C 215.00 1.510 ! NC1, qm, EH 2007, ammonium cations +ND3P3A CD33A 215.00 1.510 ! NC1, qm, EH 2007, ammonium cations +ND3P2A HDP1B 440.00 1.025 ! NH4, NMA, need work** +ND3P3A HDP1B 440.00 1.025 ! NH4, NMA, need work** +OD2C1A CD2O1A 673.70 1.245 ! NMA, N-methylacetamide %PEML jan13 +OD2C2A CD2O2A 527.00 1.250 ! ACET, CTER, PEML +OD2C1B CD2O4A 623.00 1.239 ! NA bases, jal +!! +OD2C2B PD1A 525.00 1.500 ! DMP, cmb, 06/09, lipids +!! +!jonathon/alex 2021 +OD2C3A CD2O3A 730.00 1.220 ! MAS, csd, EH 2007, PEML 2009 *** b0 should be 1.220 based on MP2/6-31g*, confirm +OD305A CD315B 350.00 1.425 ! TF2M, cmb +OD305A CD325B 350.00 1.425 ! THF, CSD/NDB survey, viv +OD306A CD326B 360.00 1.415 ! THP, tetrahydropyran, viv +OD30A CD32E 360.00 1.415 ! DEET, diethylether, alex +OD30A CD33E 360.00 1.415 ! DEET, diethylether, alex +!! +OD30B PD1A 240.00 1.600 ! DMP, lipids and nucleic acids +OD30D PD1A 240.00 1.600 ! MP_1, nucleic acid +OD30BR PD1A 240.00 1.600 ! DMP, copied for RNA, jal +!! +OD30B CD32A 335.00 1.420 ! DMP, csd, EH/IV 2007 +OD30B CD32B 335.00 1.420 ! DMP, csd, EH/IV 2007, GLYP, phosphoglycerol lipids +OD30B CD33A 335.00 1.420 ! DMP, csd, EH/IV 2007 + +OD30D CD33C 335.00 1.440 ! from DMP, for MP_1 +OD30B CD33C 335.00 1.440 ! DMP, lipids and nucleic acids +OD30BR CD33C 335.00 1.440 ! DMP, copied for RNA, jal +OD30B HDP1A 536.50 0.970 ! CHOL, MEOH, not necessary for lipid +OD30C CD2O3A 150.00 1.330 ! MAS, csd, EH 2007, PEML 2009 *** changed FC to match vibr. spectra *** +OD30C CD31C 340.00 1.440 ! MAS, csd, EH 2007 +OD30C CD32C 340.00 1.440 ! MAS, csd, EH 2007 +OD30C CD33C 340.00 1.440 ! MAS, csd, EH 2007 +OD30E CD32A 396.00 1.425 ! ETO, a&a +OD30E CD33A 480.00 1.345 ! MEO, a&a +OD31F CD2O3A 205.50 1.269 ! ACEH, PEML +OD31F HDP1A 480.40 0.969 ! ACEH, PEML +OD31A CD31A 350.00 1.440 ! PRO2, 2-propanol +OD31A CD315A 350.00 1.440 ! CPO1, cyclopropanol +OD31A CD32A 396.00 1.425 ! ETOH, ethanol +OD31A CD33B 430.00 1.425 ! MEOH, methanol +OD31A HDP1A 536.50 0.970 ! MEOH, methanol +OD31D PD1A 237.00 1.610 ! MP_1, methylphosphate +OD31B CD32A 396.00 1.425 ! ETOH, ethanol +OD31B HDP1A 536.50 0.970 ! PRO1, 1-propanol +OD31C CD2R6A 334.30 1.411 ! PHEN, phenol +OD31C HDP1A 545.00 0.960 ! PHEN, phenol +OD31D HDP1A 536.50 0.970 ! methylphosphate hydroxyl O +OD31G HDP1A 536.50 0.970 ! nucleic acid 3TER, jal +ODW HDW 450.00 0.9572 ! SWM4, SWM4-NDP water, Guillaume 2005 +ODW DOH2 500.00 0.0000 ! SWM4, SWM4-NDP water, Guillaume 2005 +HDW HDW 0.00 1.5139 ! SWM4 and SWM6 water models +ODW6 HDW 450.00 0.9572 ! SWM6-NDP water +ODW6 DOH2 500.00 0.0000 ! SWM6-NDP water +SD1A OD2C2B 525.00 1.493 ! SO4, a&a +SD1A OD30B 240.00 1.701 ! MSO4, a&a +SD1A ND2A2 185.00 1.700 ! NMSM, sulfamate, a&a +SD1A CD33C 218.00 1.823 ! MSNA, sulfonate, a&a +SD30A CD32A 228.00 1.806 ! EMS +SD30A CD33A 230.00 1.795 ! EMS +SD30B SD30B 155.50 2.036 ! DMDS +SD30B CD32A 204.10 1.806 ! DMDS, Disulfide patch +SD30B CD33A 204.10 1.806 ! DMDS +SD31A CD33A 218.00 1.811 ! MESH +SD31A HDP1A 283.00 1.3497 ! MESH +SD31B CD32A 220.00 1.810 ! ETSH +SD31B HDP1A 283.00 1.3497 ! ETSH, from 1.3497 +CD2O1A CD31A 299.30 1.467 ! CT2, ALAD, alanine dipeptide ??? CHECK THIS +CD2O1A CD31C 195.90 1.340 ! NMA, N-methylacetamide %PEML jan13 +CD2O1A CD32A 350.00 1.525 ! GLYP, GLYD, glycine dipeptide +CD2O1A CD32C 350.00 1.430 ! GLYD, PEML oct09 alterado em nov09 +CD2O1A CD33C 106.10 1.153 ! NMA, N-methylacetamide %PEML jan13 +CD2O2A CD31A 114.50 1.561 ! NTER/ACET, PEML +CD2O2A CD31C 90.00 1.560 ! CTER, PEML +CD2O2A CD32A 110.00 1.535 ! ACET, PEML +CD2O2A CD32C 90.00 1.560 ! CTER, PEML +CD2O2A CD33A 110.00 1.535 ! ACET, PEML +CD2O3A CD31A 282.20 1.505 ! ACEH/CNEU PEML +CD2O3A CD31C 108.00 1.509 ! CNEU, PEML +CD2O3A CD32C 200.00 1.510 ! MAS, csd, EH 2007, ACEH +CD2O3A CD33C 133.00 1.510 ! ACEH, PEML +CD2O4A CD2R6F 302.00 1.360 ! GUA, jal +CD2O4A CD2R6J 302.00 1.390 ! THY, jal +CD2R5A CD2R5A 410.00 1.360 ! IMID, imidazole, geom + freq, peml 2006 +CD2R5A CD2R5C 322.60 1.397 ! PYRR, pyrrole CY CA 350.000 1.3650 +CD2R5A CD32A 229.60 1.500 ! 4MIM, 4-methyl-imidazole +CD2R5A CD33A 229.60 1.500 ! 4MIM, 4-methyl-imidazole +CD2R5A HDR5A 365.00 1.083 ! IMID, imidazole, geom + freq, peml 2006 +CD2R5B HDR5B 340.00 1.090 ! IMID, imidazole, geom + freq, peml 2006 +CD2R5C CD2R5C 322.90 1.430 ! PYRR, pyrrole CY CPT 350.000 1.4400 +CD2R5C CD2R6D 407.60 1.420 ! INDO, indole +CD2R5C CD32A 229.63 1.500 ! INDM, methyl-indole, Trp +CD2R5C CD33A 229.63 1.500 ! INDM, methyl-indole +CD2R5C HDR5C 370.20 1.080 ! PYRR, pyrrole HA CY 330.000 1.0800 +CD2R5D CD2R5D 410.00 1.360 ! IMIM +CD2R5D CD32A 229.60 1.500 ! 4MIM, 4-methyl-imidazole +CD2R5D HDR5D 365.00 1.083 ! IMIM +CD2R5E HDR5E 340.00 1.090 ! IMIM +CD2R5F HDR5B 340.00 1.090 ! nucleic acids, jal +CD2R6A CD2R6A 305.00 1.375 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6A CD2R6B 361.10 1.378 ! PYR, pyridine, geom + freq, peml 2005 +CD2R6A CD2R6D 315.00 1.382 ! INDO, indole +CD2R6A CD2R6H 460.00 1.280 ! CYT, cmb 04/10 +CD2R6A CD32A 230.00 1.490 ! PHE/TOLU +CD2R6A CD33A 230.00 1.490 ! TOLU, toluene, geom + freq, peml 2005 +CD2R6A HDR6A 340.00 1.080 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6B CD2R6F 295.82 1.398 ! PUR0/1, purine +CD2R6B HDR6B 340.00 1.080 ! PYR, pyridine, geom + freq, peml 2005 +CD2R6C CD2R6F 360.00 1.358 ! ADE, cmb 04/10 +CD2R6C HDR6C 320.00 1.080 ! PYRM, pyrimidine, geom + freq, peml 2006 +CD2R6D CD2R6D 198.20 1.400 ! INDO, indole +CD2R6F CD2R6F 331.89 1.469 ! PUR0/1, purine +CD2R6H HDR6B 340.00 1.080 ! CYT, cmb 04/10 +CD2R6J CD2R6J 305.00 1.375 ! nucleic acids, jal (new atom types) +CD2R6J CD2R6B 361.10 1.378 ! nucleic acids, jal (new atom types) +CD2R6J CD2R6H 460.00 1.280 ! nucleic acids, jal (new atom types) +CD2R6J CD33A 230.00 1.490 ! nucleic acids, jal (new atom types) +CD2R6J HDR6A 340.00 1.080 ! nucleic acids, jal (new atom types) +CD30A CD32A 222.50 1.538 ! alkanes, 10/98 +CD30A CD33A 222.50 1.538 ! NEOP, neopentane, 10/98 +CD315B CD325B 195.00 1.518 ! TF2M, cmb +CD315B CD33A 222.50 1.528 ! TF2M, 2-methyl-THF,viv; mod cmb +CD315A CD33A 222.50 1.528 ! CPNM, 2-methyl-THF,viv; mod cmb +CD315B HDA1R5 307.00 1.100 ! TF2M, cmb +CD315A HDA1R5 307.00 1.100 ! CPNM, cmb by analogy +CD31A CD31A 222.50 1.500 ! alkanes, 3/92 +CD31A CD31C 222.50 1.500 ! 3/92 +CD31A CD32A 222.50 1.538 ! alkanes, 3/92 +CD31A CD33A 225.00 1.538 ! va, 9/07 +CD31A HDA1A 309.00 1.111 ! IBUT, isobutane, alkanes, 4/98 +CD31A HDA1C 300.00 1.080 ! NTER, NC4, qm, EH 2007, From CD33A HDA3C +CD31C HDA1C 300.00 1.080 ! NTER, NC4, qm, EH 2007, From CD33A HDA3C +CD31C CD31C 222.50 1.500 ! alkane +CD31C CD32A 222.50 1.528 ! 3/92 %PEML oct09 alterado em nov09 +CD31C CD32B 222.50 1.528 ! GLU, from CD31C CD32A, GLYP, phosphoglycerol lipids +CD31C CD32C 222.50 1.528 ! 3/92 ??? CHECK THIS +CD31C CD33A 180.40 1.541 ! 3/92 %PEML jan13 +CD31C CD33C 222.50 1.528 ! alkane ??? CHECK THIS +CD31C HDA1A 309.00 1.111 ! alkanes, 4/98 +CD325A CD325A 195.00 1.548 ! CPEN, cyclopentane, viv +CD315A CD325A 195.00 1.548 ! CPNM, from CPEN, cmb +CD325A HDA2R5 307.00 1.116 ! CPEN, cyclopentane, viv +CD325B CD325B 195.00 1.518 ! THF, CSD/NDB survey, viv +CD325B HDA2R5 307.00 1.100 ! THF, THF neutron diffr, viv +CD316A CD326A 222.50 1.530 ! CHXM, from alkanes CD32A, cmb 12/09 +CD316A HDA1A 309.00 1.111 ! CHXM, from alkanes CD32A, cmb 12/09 +CD316A CD33A 225.00 1.538 ! CHXM, from va, 9/07. cmb 12/09 +CD326A CD326A 222.50 1.530 ! CHEX, from alkanes CD32A, cmb 9/09 +CD326A HDA2A 309.00 1.111 ! CHEX, from alkanes CD32A, cmb 9/09 +CD326B CD326B 222.50 1.530 ! THP, tetrahydropyran, viv +CD326B HDA2E 309.00 1.111 ! THP, tetrahydropyran, viv +CD32A CD32A 222.50 1.530 ! alkanes, 3/92 +CD32A CD32B 222.50 1.530 ! GLU, from CD32A CD32A +CD32B CD32C 222.50 1.530 ! GLUP, from CD32A CD32A +CD32A CD32C 222.50 1.530 ! alkane +CD32A CD32E 222.50 1.530 ! ethers +CD32A CD33A 222.50 1.528 ! alkanes, 3/92 +CD32A CD33C 222.50 1.528 ! alkane +CD32A HDA2A 309.00 1.111 ! alkanes, 4/98 +CD32B HDA2A 309.00 1.111 ! GLU, from CD32A HDA2A +CD32A HDA2C 300.00 1.080 ! GLYP, NC4, qm, EH 2007 +CD32C HDA2C 300.00 1.080 ! GLYP, NC4, qm, EH 2007 +CD32C CD32C 222.50 1.530 ! alkane +CD32C CD33A 222.50 1.528 ! alkane +CD32C CD33C 222.50 1.528 ! alkane +CD32C HDA2A 309.00 1.111 ! 4/98 +!revert_lipids +!CD32C CD2O3B 200.00 1.510 ! MAS, csd, EH 2007, ACEH +CD32E CD32E 222.50 1.530 ! ethers +CD32E CD33A 222.50 1.528 ! ethers +CD32E HDA2E 309.00 1.111 ! ethers, cmb +CD33A CD33A 222.50 1.530 ! alkanes, 3/92 +CD33A HDA3A 322.00 1.111 ! alkanes, 4/98 +CD33A HDA3C 300.00 1.080 ! NC4, qm, EH 2007, ammonium cations +CD33B HDA3B 322.00 1.111 ! alkanes, 4/98, MEOH, methanol special case +CD33C CD33C 222.50 1.530 ! alkane +CD33C HDA3A 322.00 1.111 ! 4/98 +CD33E HDA3A 322.00 1.111 ! ethers +!alkenes +CD2C1A CD32A 325.30 1.5000 ! BTE1, PTE1, HXE1; pc 06/2022 +CD2C1A CD33A 333.90 1.5100 ! 2BTE pc 06/2022 +CD2C1A CD2C1A 650.90 1.3500 ! 2BTE1,2PTE,2HEX, all 2-alkenes; pc 06/2022 +CD2C1A CD2C1B 489.90 1.3364 ! ETHE, PRPE, BTE1 , PTE1, HXE1 ; pc 06/2022 +CD2C1B CD2C1B 489.90 1.3364 ! ETHE;pc 06/2022 +CD2C1A HD2C1A 464.60 1.1000 ! 2BTE, PTE1, 2PTE, 2HEX, HXE1 ; pc 06/2022 +CD2C1B HD2C1B 354.60 1.0907 ! ETHE, PRPE, BTE1, PTE1, HXE1; pc 06/2022 +CD2C1A CD326A 360.300 1.4950 ! CHXE ; PC 06/2022 + +!alkenes end +!carbonyls +CD2O1C CD31C 245.00 1.491 ! +OD2C1D LPDO1 0.00 0.000 ! FORM +OD2C1D CD2O1C 750.00 1.218 ! FORM +OD2C1D CD2O1D 750.00 1.218 ! +CD2O1D CD33C 250.00 1.498 ! +CD2O1D CD32C 245.00 1.491 ! +CD2O1C HDP1C 310.00 1.104 ! +OD2C1C CD2O1C 750.00 1.218 ! +CD2O1C CD33C 250.00 1.498 ! +CD2O1C CD32C 245.00 1.491 ! +CD2O1C CD31G 245.00 1.491 ! from CD2O1C CD32C +CD2O1D CD32F 250.00 1.498 ! from CD2O1D CD33C +CD2O1D CD31G 245.00 1.491 ! from CD2O1D CD32C +CD32F LPD 0.00 0.000 ! +CD31G LPD 0.00 0.000 ! glycerol, xhe +!carbonyls end +! +X DRUD 500.00 0.000 ! DO NOT COMMENT. Essential for use of Drudes in c46b1 and maybe more. Bug... +! +ODW LPDW 0.00 0.24034492 ! SWM4, SWM4-NDP water, Guillaume 2005 +DOH2 LPDW 500.00 0.000 ! SWM4 and SWM6 water models +ODW6 LPDW 0.00 0.000 ! SWM6-NDP water +HDP1A LPD 0.00 0.000 ! ACEH, PEML +CD2O1A LPD 0.00 0.000 ! NMA +CD2O1C LPD 0.00 0.000 ! +CD2O1D LPD 0.00 0.000 ! +CD2O2A LPD 0.00 0.000 ! Acetate +CD2O3A LPD 0.00 0.000 ! MAS +CD2O4A LPD 0.00 0.000 ! jal +CD2R5A LPD 0.00 0.000 ! IMID +CD2R5B LPD 0.00 0.000 ! IMID +CD2R5F LPD 0.00 0.000 ! jal +CD2R6A LPD 0.00 0.000 ! PHEN +CD2R6B LPD 0.00 0.000 ! PYR +CD2R6C LPD 0.00 0.000 ! PYRM +CD2R6F LPD 0.00 0.000 ! PUR0/1 +CD2R6H LPD 0.00 0.000 ! CYT,THY,URA, cmb 04/10 +CD2R6J LPD 0.00 0.000 ! jal +CD315B LPD 0.00 0.000 ! TF2M +CD31A LPD 0.00 0.000 ! PRO2 +CD31C LPD 0.00 0.000 ! MAS +CD325B LPD 0.00 0.000 ! THF +CD326B LPD 0.00 0.000 ! DMP +CD32A LPD 0.00 0.000 ! DEET +CD32C LPD 0.00 0.000 ! MAS +CD32E LPD 0.00 0.000 ! DEET +CD33A LPD 0.00 0.000 ! DMP +CD33B LPD 0.00 0.000 ! MEOH +CD33C LPD 0.00 0.000 ! MAS +CD33E LPD 0.00 0.000 ! DMP +ND2R5B LPD 0.00 0.000 ! IMID +ND2R5B LPDNA1 0.00 0.000 ! Purine +ND2R5E LPDNA1 0.00 0.000 ! GUA/ADE, cmb 04/10 +ND2R6A LPDNA1 0.00 0.000 ! PYR +ND2R6B LPDNA1 0.00 0.000 ! PYRM +OD2C1A LPD 0.00 0.000 ! NMA +OD2C1A LPDO1 0.00 0.000 ! NMA, special LP +OD2C1C LPD 0.00 0.000 ! +OD2C1D LPD 0.00 0.000 ! +OD2C2A LPD 0.00 0.000 ! Acetate, DMP +OD2C1B LPDNA1 0.00 0.000 ! NA bases, cmb 04/10 +OD2C3A LPD 0.00 0.000 ! MAS +OD305A LPD 0.00 0.000 ! THF +OD306A LPD 0.00 0.000 ! THP +OD30A LPD 0.00 0.000 ! DEET +OD30B LPD 0.00 0.000 ! DMP +OD30C LPD 0.00 0.000 ! MAS +OD31F LPD 0.00 0.000 ! ACEH, PEML +OD31A LPD 0.00 0.000 ! ETOH +OD31A LPDNA1 0.00 0.000 ! nucleic acids +OD31D LPDNA1 0.00 0.000 ! ETOH, for MP_1 +OD31B LPD 0.00 0.000 ! PRO1 +OD31C LPD 0.00 0.000 ! PHEN +OD31G LPD 0.00 0.000 ! jal +SD30A LPD 0.00 0.000 ! EMS, DMS +SD30B LPD 0.00 0.000 ! DMDS +SD31A LPD 0.00 0.000 ! MESH +SD31B LPD 0.00 0.000 ! ETSH +PD1A LPD 0.00 0.000 ! DMP, nucleic acid + +ANGLES +!atom types Ktheta Theta0 Kub S0 +!================================================== +CD2O1A ND2A1 HDP1A 50.00 123.50 ! ACEM +HDP1A ND2A1 HDP1A 24.00 113.00 ! ACEM +CD2O1C ND2A1 HDP1A 50.00 117.00 ! FORM +CD2O1A ND2A2 CD31C 40.90 116.10 ! ALAD % +CD2O1A ND2A2 CD32C 80.20 121.00 ! GLYD +CD2O1A ND2A2 CD33C 97.70 120.77 ! NMA+ALAD % +CD2O1A ND2A2 HDP1A 45.60 120.26 ! NMA+ALAD % +CD31C ND2A2 HDP1A 72.20 123.64 ! ALAD % +CD32C ND2A2 HDP1A 64.50 119.00 ! GLYD +CD33C ND2A2 HDP1A 48.00 118.97 ! NMA+ALAD % +CD2O1A ND2A3 CD33C 10.00 119.20 ! DMA +CD33C ND2A3 CD33C 40.00 121.60 ! DMA +CD31C ND3A2 HDP1A 40.00 109.30 ! NNEU, based on HDP1A ND3A2 CD32A, eam1, fylin +CD32C ND3A2 HDP1A 40.00 109.30 ! NNEU-Gly, based on HDP1A ND3A2 CD32A, eam1, fylin +CD32C ND3A3 HDP1A 64.50 119.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ?? +CD2N1A ND2P1A CD32A 62.30 120.00 ! ARG, c22 +CD2N1A ND2P1A CD33A 62.39 120.00 ! GUAN, c22 +CD2N1A ND2P1A HDP1B 49.00 124.00 ! GUAN, geo opt (EH) +CD32A ND2P1A HDP1B 40.40 120.00 ! ARG, c22 +CD33A ND2P1A HDP1B 40.40 120.00 ! GUAN, c22 +HDP1B ND2P1A HDP1B 25.00 114.00 ! GUAN, geo opt (EH) +CD2R5A ND2R5A CD2R5A 119.08 106.00 ! PYRR, pyrrole +CD2R5A ND2R5A CD2R5B 130.00 107.50 ! IMID, imidazole +CD2R5A ND2R5A CD2R6D 81.40 108.60 ! INDO, indole +CD2R5A ND2R5A HDP1A 30.00 125.50 20.00 2.1500 ! IMID, imidazole +CD2R5B ND2R5A CD2R6F 137.46 109.60 ! PUR0/1, purine +CD2R5B ND2R5A HDP1A 30.00 127.00 20.00 2.1400 ! IMID, imidazole +CD2R6D ND2R5A HDP1A 12.80 125.90 ! INDO, indole +CD2R6F ND2R5A HDP1A 37.59 125.50 28.70 2.2021 ! PUR0/1, purine +CD2R5A ND2R5B CD2R5B 130.00 104.00 ! IMID, imidazole +CD2R5A ND2R5B CD2R5F 130.00 104.00 ! jal +CD2R5B ND2R5B CD2R6F 127.91 103.00 ! PUR0/1, purine +CD2R5F ND2R5B CD2R6F 127.91 103.00 ! jal +CD2R5B ND2R5D CD32A 17.00 127.80 ! Et-Gua, cmb 04/10 +CD2R5F ND2R5D CD32A 17.00 127.80 ! Et-Gua, jal +CD2R5A ND2R5C HDP1A 25.00 126.00 15.00 2.1300 ! IMID, imidazole +CD2R5B ND2R5C HDP1A 25.00 126.00 15.00 2.0900 ! IMID, imidazole +CD2R5D ND2R5C CD2R5E 130.00 111.00 ! IMIM, geo opt (EH) +CD2R5D ND2R5C HDP1A 30.000 125.50 20.00 2.1500 ! IMIM +CD2R5E ND2R5C HDP1A 30.000 127.00 20.00 2.1400 ! IMIM +CD2R5B ND2R5D HDP1A 30.00 127.00 20.00 2.1400 ! ADE/IMID, imidazole +CD2R5F ND2R5D HDP1A 30.00 127.00 20.00 2.1400 ! ADE/IMID, imidazole, jal +CD2R6F ND2R5D HDP1A 28.00 126.00 ! ADE, cmb 04/10 +CD2R6F ND2R5D CD32A 17.00 125.90 ! Et-Gua, cmb 04/10 +CD2R6B ND2R6A CD2R6B 19.60 100.00 54.20 2.2850 ! PYR, pyridine +CD2O4A ND2R6B CD2R6H 100.00 118.00 ! CYT, jal +CD2O4A ND2R6C CD33A 60.00 115.40 ! CYT, jal +CD2O4A ND2R6B HDP1A 37.00 121.20 ! CYT, jal +CD2R6B ND2R6B CD2R6C 27.50 110.00 66.70 2.2000 ! PYRM, pyrimidine +CD2R6C ND2R6B CD2R6F 26.30 121.10 75.00 2.3797 ! PUR0/1, purine (for model cmpds?) +CD2R6H ND2R6C CD33A 60.00 120.50 ! CYT, cmb 04/10 +CD2R6H ND2R6C HDP1A 37.00 114.70 ! CYT, cmb 04/10 +CD2R6C ND2R6C HDP1A 45.00 115.60 ! GUA, cmb 04/10 +CD2O1A ND3A3 CD31C 35.00 111.00 ! PRO +CD2O1A ND3A3 CD32A 35.00 111.00 ! PRO +CD31C ND3A3 CD32A 50.00 111.00 ! PRO +CD32C ND3A3 CD32C 50.00 111.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ?? +CD32A ND3P2A CD31C 60.00 109.50 26.00 2.4660 ! NC4, qm, EH 2007, ammonium cations, +CD32A ND3P2A CD33A 60.00 109.50 26.00 2.4660 ! NC4, qm, EH 2007, ammonium cations +CD33A ND3P2A CD33A 60.00 109.50 26.00 2.4660 ! NC4, qm, EH 2007, ammonium cations +CD31A ND3P2A HDP1B 28.80 113.10 11.30 1.983 ! NTER, PEML +CD31C ND3P2A HDP1B 28.80 113.10 11.30 1.983 ! NTER, PEML +CD32A ND3P2A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +CD32C ND3P2A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +CD33A ND3P2A HDP1B 33.00 109.50 4.00 2.0560 ! NC1, charmm27 (etam), ammonium cations +HDP1B ND3P2A HDP1B 41.00 109.50 ! NH4, charmm27, ammonium cations +CD31A ND3P3A HDP1B 28.80 113.10 11.30 1.983 ! NTER, PEML +CD31C ND3P3A HDP1B 28.80 113.10 11.30 1.983 ! NTER, PEML +CD32A ND3P3A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +CD32C ND3P3A HDP1B 33.00 109.50 4.00 2.0560 ! ETAM, charmm27, ammonium cations +CD33A ND3P3A HDP1B 33.00 109.50 4.00 2.0560 ! NC1, charmm27 (etam), ammonium cations +HDP1B ND3P3A HDP1B 41.00 109.50 ! NH4, charmm27, ammonium cations +CD315B OD305A CD325B 95.00 111.00 ! TF2M 02/09, cmb +CD325B OD305A CD325B 95.00 111.00 ! THF, viv 10/21/05 +CD326B OD306A CD326B 95.00 109.70 ! THP, viv +CD32A OD30A CD32A 95.00 109.70 ! DEET, diethylether, alex +CD32A OD30A CD33A 95.00 109.70 ! DEET, diethylether, alex +CD32E OD30A CD32E 95.00 109.70 ! DEET, diethylether, alex +CD32E OD30A CD33E 95.00 109.70 ! DEET, diethylether, alex +CD33A OD30A CD33A 95.00 109.70 ! DME dimethylether,viv +CD33E OD30A CD33E 95.00 109.70 ! DME dimethylether,viv +!! +PD1A OD30B CD32A 40.00 112.50 ! DMP, lipids & nucleic acids +PD1A OD30B CD32B 40.00 112.50 ! GLYP, phosphoglycerol lipids +PD1A OD30BR CD32A 40.00 112.50 ! DMP, csd, nucleic acids, copied for RNA (jal) +PD1A OD30B CD33A 40.00 112.50 ! DMP, lipids & nucleic acids +PD1A OD30BR CD33A 40.00 112.50 ! DMP, csd, nucleic acids, copied for RNA (jal) +PD1A OD30D CD33C 40.00 120.50 ! from DMP, nucleic acids, for MP_1 +PD1A OD30B CD33C 40.00 120.50 ! DMP, lipids & nucleic acids +PD1A OD30BR CD33C 40.00 120.50 ! DMP, cmb, nucleic acids, copied for RNA (jal) +!! +!jonathon/alex 2021, Yalun opt, 2022 +CD2O3A OD30C CD31C 90.00 114.50 ! GLYC, QM +CD2O3A OD30C CD32C 90.00 114.50 ! EAS, QM +CD2O3A OD30C CD33C 20.00 90.00 ! MAS, QM +! +CD2O3A OD31F HDP1A 58.90 110.20 15.10 2.3770 ! ACEH, PEML +CD2O3A CD32C HDA2A 33.00 109.50 30.00 2.1630 ! MPO, charmm27 +CD2O3A CD33C HDA3A 33.00 109.50 30.00 2.1630 ! MAS, charmm27 +CD2O3A CD32C CD33A 52.00 108.00 ! MPO, alkane +CD2O3A CD32C CD32A 52.00 108.00 ! MBU, alkane +CD2R6A OD31A HDP1A 65.00 108.00 ! PHE, Phenol +CD31A OD31A HDP1A 59.00 108.00 ! PRO2, 2-propanol +CD315A OD31A HDP1A 59.00 108.00 ! CPO1, cyclohexanol +CD32A OD31A HDP1A 49.00 106.00 ! ETOH, ethanol +CD33B OD31A HDP1A 58.20 106.00 ! MEOH, methanol +CD32A OD31B HDP1A 49.00 106.00 ! PRO1, 1-propanol +CD2R6A OD31C HDP1A 65.00 108.00 ! PHEN, Phenol +HDW ODW HDW 55.000 104.52 ! SWM4-NDP water Guillaume 2005 +HDW ODW6 HDW 55.000 104.52 ! SWM6-NDP water model +CD32A SD30A CD33A 21.00 97.10 ! EMS +CD33A SD30A CD33A 21.00 97.10 ! DMS +SD30B SD30B CD32A 60.00 104.25 ! DMDS, Disulfide patch +SD30B SD30B CD33A 60.00 104.25 ! DMDS +CD33A SD31A HDP1A 40.00 96.10 ! MESH +CD32A SD31B HDP1A 45.80 96.48 ! ETSH +ND2P1A CD2N1A ND2P1A 52.00 120.00 90.00 2.3642 ! GUAN, geo opt (EH) +ND2A1 CD2O1A OD2C1A 85.00 125.00 ! ACEM +ND2A1 CD2O1A CD31C 62.37 110.66 ! CT2 +ND2A1 CD2O1A CD32C 40.00 114.00 ! ASN, Acetamide +ND2A1 CD2O1A CD33C 40.00 114.00 ! ACEM +ND2A2 CD2O1A OD2C1A 89.70 130.90 ! NMA+ALAD % important for N-C=O +ND2A2 CD2O1A CD31A 62.37 110.66 ! NTER-(X)n-CNEU +ND2A2 CD2O1A CD31C 74.80 102.10 174.4 2.6308 ! ALAD % important for Ca-C-N (dCT-C-N) +ND2A2 CD2O1A CD32A 62.37 110.66 ! NTER-(X)n-CNEU +ND2A2 CD2O1A CD32C 92.10 114.70 179.80 2.4290 ! GLYD % +ND2A2 CD2O1A CD33C 51.50 109.82 84.40 2.9072 ! NMA+ALAD % important for Ca-C-N +ND2A3 CD2O1A OD2C1A 70.00 123.00 ! DMA +ND2A3 CD2O1A CD33C 70.00 115.00 ! DMA +ND2R6B CD2O4A ND2R6B 50.00 113.00 ! CYT, va, jal +ND3A2 CD31C HDA1A 65.00 110.50 ! NNEU, based on ND3A2 CD32A HDA2A, eam1, fylin +ND3A2 CD32C HDA2A 65.00 110.50 ! NNEU-Gly, based on ND3A2 CD32A HDA2A, eam1, fylin +ND3A2 CD31C CD31A 65.00 111.95 ! NNEU, based on ND3A2 CD32A CD33A, eam1, fylin +ND3A2 CD31C CD32A 65.00 111.95 ! NNEU, based on ND3A2 CD32A CD33A, eam1, fylin +ND3A2 CD31C CD32B 65.00 111.95 ! NNEU, based on ND3A2 CD32A CD33A, eam1, fylin +ND3A2 CD31C CD32C 65.00 111.95 ! NNEU, based on ND3A2 CD32A CD33A, eam1, fylin +ND3A2 CD31C CD33A 65.00 111.95 ! NNEU, based on ND3A2 CD32A CD33A, eam1, fylin +ND3A2 CD31C CD2O1A 78.50 97.50 ! NNEU, based on NTER, PEML +ND3A2 CD32C CD2O1A 78.50 97.50 ! NNEU-Gly, based on NTER, PEML +ND3A3 CD2O1A CD31C 63.37 108.69 ! 62.00 110.00 ! PRO, uncommented, zhu +ND3A3 CD2O1A CD32A 63.37 108.69 ! 62.00 110.00 ! PRO, uncommented, zhu +ND3A3 CD2O1A CD32C 63.37 108.69 ! 62.00 110.00 ! PRO, uncommented, zhu +ND3A3 CD2O1A CD33C 63.37 108.69 ! 62.00 110.00 ! PRO +ND3A3 CD2O1A OD2C1A 66.19 129.68 ! 62.00 110.00 ! PRO +OD2C1A CD2O1A CD31A 69.30 111.80 ! NTER-(X)n-CNEU +OD2C1A CD2O1A CD31C 96.00 127.00 107.6 2.4358 ! ALAD % important for Ca-C=O (dC=O) +OD2C1A CD2O1A CD32A 69.30 111.80 ! NTER-(X)n-CNEU +OD2C1A CD2O1A CD32C 110.40 116.20 180.10 2.4180 ! GLYD ??? CHECK +OD2C1A CD2O1A CD33C 59.20 116.10 81.70 2.4774 ! NMA+ALAD % important for Ca-C=O (dC=O) +ND2A1 CD2O1C OD2C1D 45.00 127.00 50.00 2.3700 ! FORM, fylin +ND2A1 CD2O1C HDP1C 35.00 115.00 50.00 1.9800 ! FORM, fylin +OD2C2A CD2O2A OD2C2A 83.70 127.90 128.80 2.3790 ! ACET, PEML +OD2C2A CD2O2A CD31A 40.00 109.30 ! NTER, PEML +OD2C2A CD2O2A CD31C 48.90 123.00 29.90 2.2930 ! CTER, PEML, ACET +OD2C2A CD2O2A CD32A 48.90 123.00 29.90 2.2930 ! CTER, PEML, ACET +OD2C2A CD2O2A CD32C 40.00 109.30 ! NTER, PEML, terminal Gly +OD2C2A CD2O2A CD33A 23.80 123.00 34.90 2.3910 ! ACET, PEML +!! +OD2C2B PD1A OD2C2B 120.00 125.00 ! DMP, lipids & nucleic acids +OD2C2B PD1A OD30D 98.90 113.00 ! MP_1 +OD2C2B PD1A OD30B 98.90 113.00 ! DMP, lipids & nucleic acids +OD2C2B PD1A OD30BR 98.90 113.00 ! for RNA (jal) +OD30B PD1A OD30B 90.00 107.50 ! DMP, lipids & nucleic acids +OD30BR PD1A OD30B 90.00 107.50 ! for RNA (jal), to master +!! +OD30D PD1A OD31D 48.10 108.00 ! MP_1 specific +PD1A OD31D HDP1A 30.00 115.00 40.00 2.3500 ! MP_1 specific +OD31D PD1A OD2C2B 98.90 111.00 ! MP_1 specific +OD31D PD1A OD31D 98.90 104.0 ! MP_0 specific, c36 +! +CD32C OD30B PD1A 40.00 124.50 ! nucleic acids +CD315B OD30B PD1A 40.00 114.50 ! nucleic acids +CD315B OD30BR PD1A 40.00 114.50 ! for RNA (jal) +!! +OD2C3A CD2O3A OD30C 90.00 123.00 160.00 2.2576 ! MAS, csd, EH 2007 +OD2C3A CD2O3A OD31F 98.80 117.50 178.30 2.4240 ! ACEH, PEML +OD2C3A CD2O3A CD31A 80.00 121.00 39.90 2.412 ! NTER, PEML +OD2C3A CD2O3A CD31C 50.50 123.20 33.10 2.226 ! CNEU +OD2C3A CD2O3A CD32C 70.00 126.00 20.00 2.4420 ! MAS, csd, EH 2007 +OD2C3A CD2O3A CD33C 70.00 126.00 20.00 2.4420 ! MAS, csd, EH 2007 +OD30C CD2O3A CD31C 55.00 111.00 20.00 2.3260 ! MAS, csd, EH 2007 +OD30C CD2O3A CD32C 55.00 111.00 20.00 2.3260 ! MAS, csd, EH 2007 +OD30C CD2O3A CD33C 55.00 111.00 20.00 2.3260 ! MAS, csd, EH 2007 +OD31F CD2O3A CD31A 65.00 107.30 26.80 2.253 ! NTER, PEML +OD31F CD2O3A CD31C 46.20 115.70 36.00 2.126 ! CNEU +OD31F CD2O3A CD32C 46.20 115.70 36.00 2.126 ! CNEU +OD31F CD2O3A CD33C 48.50 113.40 26.80 2.3370 ! ACEH, PEML +ND2R5A CD2R5A CD2R5A 130.00 106.00 ! IMID, imidazole +ND2R5A CD2R5A CD2R5C 100.02 106.00 28.00 2.2400 ! PYRR, pyrrole +ND2R5A CD2R5A CD32A 45.80 124.00 ! HSD, 4MIM, 4-methyl-imidazole +ND2R5A CD2R5A CD33A 45.80 124.00 ! 4MIM, 4-methyl-imidazole +ND2R5A CD2R5A HDR5A 25.00 124.00 20.00 2.1400 ! IMID, imidazole +ND2R5B CD2R5A CD2R5A 130.00 110.00 ! IMID, imidazole +ND2R5B CD2R5A CD32A 45.800 120.00 ! HSE, c22 +ND2R5B CD2R5A CD33A 45.800 120.00 ! 4MIE, fylin +ND2R5B CD2R5A HDR5A 25.00 120.00 20.00 2.1400 ! IMID, imidazole +ND2R5C CD2R5A CD32A 45.800 122.00 ! HSP, c22 +CD2R5A CD2R5A CD32A 45.80 130.00 ! HSD, 4MIM, 4-methyl-imidazole +CD2R5A CD2R5A CD33A 45.80 130.00 ! 4MIM, 4-methyl-imidazole +CD2R5A CD2R5A HDR5A 25.00 130.00 20.00 2.2000 ! IMID, imidazole +CD2R5A CD2R5A HDR5B 22.00 130.00 15.00 2.2150 ! IMID, imidazole +CD2R5C CD2R5A HDR5A 18.63 125.00 28.00 2.1730 ! PYRR, pyrrole +ND2R5A CD2R5B ND2R5B 130.00 112.50 ! IMID, imidazole +ND2R5A CD2R5B HDR5B 25.00 122.50 20.00 2.1400 ! IMID, imidazole +ND2R5B CD2R5B HDR5B 25.00 125.00 20.00 2.1200 ! IMID, imidazole +ND2R5B CD2R5F HDR5B 25.00 125.00 20.00 2.1200 ! jal +ND2R5D CD2R5B HDR5B 25.00 122.50 20.00 2.1400 ! ADE/IMID, imidazole +ND2R5D CD2R5F HDR5B 25.00 122.50 20.00 2.1400 ! jal +ND2R5E CD2R5F HDR5B 25.00 125.00 20.00 2.1200 ! ADE, jal +CD2R5A CD2R5C CD2R5C 80.00 106.40 27.90 2.2610 ! PYRR, pyrrole +CD2R5A CD2R5C CD2R6D 81.90 106.10 22.50 2.2163 ! INDO, indole +CD2R5A CD2R5C CD32A 45.80 122.30 ! INDM, methyl-indole, Trp +CD2R5A CD2R5C CD33A 45.80 122.30 ! INDM, methyl-indole +CD2R5A CD2R5C HDR5C 12.72 126.40 28.00 2.2150 ! PYRR, pyrrole +CD2R5C CD2R5C HDR5C 23.80 126.40 28.00 2.2150 ! PYRR, pyrrole +CD2R6D CD2R5C CD32A 45.80 122.30 ! INDM, methyl-indole, Trp +CD2R6D CD2R5C CD33A 45.80 122.30 ! INDM, methyl-indole +CD2R6D CD2R5C HDR5C 1.70 124.70 8.39 2.3781 ! INDO, indole +ND2R5C CD2R5D CD2R5D 130.00 105.50 ! IMIM, geo opt (EH) +ND2R5C CD2R5D CD32A 45.80 124.00 ! HSP, 4MIM, 4-methyl-imidazole +ND2R5C CD2R5D HDR5D 25.00 124.00 20.00 2.1400 ! IMIM, from IMID (EH) +CD2R5D CD2R5D CD32A 45.80 130.00 ! HSP, 4MIM, 4-methyl-imidazole +CD2R5D CD2R5D HDR5D 25.000 130.00 20.00 2.2000 ! IMIM +ND2R5C CD2R5E ND2R5C 130.00 107.75 ! IMIM, geo opt (EH) +ND2R5C CD2R5E HDR5E 25.00 125.00 20.00 2.1200 ! IMIM, from IMID (EH) +OD31A CD2R6A CD2R6A 45.20 120.00 ! PHE, Phenol +OD31C CD2R6A CD2R6A 45.20 120.00 ! PHEN, Phenol +CD2R6A CD2R6A CD2R6A 40.00 120.00 35.00 2.4162 ! BENZ, benzene +CD2R6A CD2R6A CD2R6B 46.10 120.00 29.80 2.4480 ! PYR, pyridine +CD2R6A CD2R6A CD2R6D 143.50 123.80 ! INDO, indole +CD2R6A CD2R6A CD32A 45.80 122.30 ! PHE/TOLU +CD2R6A CD2R6A CD33A 45.80 122.30 ! TOLU, toluene +CD2R6A CD2R6A HDR6A 30.00 120.00 22.00 2.1525 ! BENZ, benzene +CD2R6B CD2R6A CD2R6B 60.20 128.00 33.20 2.4400 ! PYRM, pyrimidine +CD2R6B CD2R6A HDR6A 26.00 120.00 21.00 2.1525 ! PYR, pyridine +CD2R6D CD2R6A HDR6A 43.50 122.60 19.90 2.0833 ! INDO, indole +CD2R6H CD2R6A CD33A 38.00 124.60 ! THY, cmb +CD2R6H CD2R6A HDR6A 30.00 117.50 ! CYT, cmb +ND2R6A CD2R6B CD2R6A 27.40 119.20 ! PYR, pyridine +ND2R6A CD2R6B HDR6B 25.90 112.00 32.20 2.0500 ! PYR, pyridine +ND2R6B CD2R6B CD2R6A 44.30 121.00 ! nucleic acids, from 125.00 ! PYRM, pyrimidine +ND2R6B CD2R6B CD2R6F 23.16 123.30 ! PUR0/1, purine +ND2R6B CD2R6B HDR6B 28.40 112.00 23.90 2.0500 ! PYRM, pyrimidine +CD2R6A CD2R6B HDR6B 43.40 120.00 18.60 2.1525 ! PYR, pyridine +CD2R6F CD2R6B HDR6B 13.06 105.10 27.60 2.1019 ! PUR0/1, purine +CD2O4A CD2R6J CD33A 38.00 118.70 ! THY, jal +CD2O4A CD2R6J HDR6A 30.00 120.30 ! URA, jal +CD2R6B CD2R6J CD2R6B 60.20 128.00 33.20 2.4400 ! PYRM, pyrimidine +CD2R6B CD2R6J HDR6A 26.00 120.00 21.00 2.1525 ! PYR, pyridine +CD2R6D CD2R6J HDR6A 43.50 122.60 19.90 2.0833 ! INDO, indole +CD2R6H CD2R6J CD33A 38.00 124.60 ! THY +CD2R6H CD2R6J HDR6A 30.00 117.50 ! CYT +ND2R6A CD2R6B CD2R6J 27.40 119.20 ! PYR, pyridine +ND2R6B CD2R6B CD2R6J 44.30 121.00 ! nucleic acids, from 125.00 ! PYRM, pyrimidine +CD2R6J CD2R6B HDR6B 43.40 120.00 18.60 2.1525 ! PYR, pyridine +ND2R5D CD32A HDA2A 33.43 107.00 ! Et-Gua, cmb 04/10 +ND2R5D CD32A CD33A 43.43 107.00 ! Et-Gua, cmb 04/10 +ND2R6B CD2R6C ND2R6B 17.00 141.00 ! nucleic acids, from 135.00 ! PYRM, pyrimidine +ND2R6B CD2R6C HDR6C 28.40 112.00 23.90 2.0500 ! PYRM, pyrimidine +ND2R5A CD2R6D CD2R6A 132.10 130.90 ! INDO, indole +ND2R5A CD2R6D CD2R6D 31.40 105.50 ! INDO, indole +CD2R5C CD2R6D CD2R6A 144.30 130.90 ! INDO, indole +CD2R5C CD2R6D CD2R6D 81.90 106.10 22.59 2.2163 ! INDO, indole +CD2R6A CD2R6D CD2R6D 50.10 126.50 ! INDO, indole +ND2R5A CD2R6F ND2R6B 130.00 110.00 ! PUR0, purine tautomer B +ND2R5A CD2R6F CD2R6B 130.00 110.00 ! PUR1, purine tautomer A +ND2R5A CD2R6F CD2R6F 111.40 96.00 ! PUR0/1, purine +ND2R5B CD2R6F ND2R6B 130.00 110.00 ! PUR1, purine tautomer A +ND2R5E CD2R6F ND2R6B 130.00 110.00 ! ADE, cmb 04/10 +ND2R5B CD2R6F CD2R6B 130.00 110.00 ! PUR0, purine tautomer B +ND2R5E CD2R6F CD2R6B 130.00 110.00 ! ADE, cmb 04/10 +ND2R5B CD2R6F CD2R6F 99.82 101.50 ! PUR0/1, purine +ND2R6B CD2R6F CD2R6F 29.82 120.50 ! nucleic acids, from 100.50 ! PUR0/1, purine (model compounds) +CD2R5B CD2R6F CD2R6F 58.07 117.30 9.20 2.3476 ! PUR0/1, purine +CD2R5F CD2R6F CD2R6F 58.07 117.30 9.20 2.3476 ! jal +CD2R6B CD2R6F CD2R6F 79.82 109.20 4.50 2.2904 ! PUR0/1, purine +ND2R6B CD2R6H CD2R6A 10.00 115.00 ! CYT, cmb +ND2R6B CD2R6H CD2R6J 10.00 115.00 ! CYT, jal +ND2R6C CD2R6H HDR6B 30.00 116.00 ! CYT, cmb 04/10 +CD2R6A CD2R6H HDR6B 30.00 122.00 ! CYT, cmb +CD2R6J CD2R6H HDR6B 30.00 122.00 ! CYT, jal +CD32A CD30A CD32A 58.35 113.50 11.16 2.561 ! glycerol ? need check +CD33A CD30A CD33A 53.35 114.00 8.00 2.561 ! alkane 3/2/92 ? need check +CD33A CD30A CD32A 53.35 114.00 8.00 2.561 ! alkane 3/2/92 ? need check +OD305A CD315B CD325B 45.00 111.10 ! TF2M 02/09, cmb +OD305A CD315B CD33A 45.00 111.50 ! TF2M, viv; cmb +OD305A CD315B HDA1R5 70.00 107.30 ! TF2M 02/09, cmb +CD325B CD315B CD325B 58.00 109.50 11.16 2.561 ! TF2M 02/09, cmb +CD325B CD315B CD33A 53.35 114.00 8.00 2.561 ! TF2M, cmb +CD325A CD315A CD33A 53.35 114.00 8.00 2.561 ! CPNM, cmb +CD325A CD315A OD31A 53.35 114.00 8.00 2.561 ! CPO1, cmb +CD325B CD315B HDA1R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +CD325A CD315A HDA1R5 35.00 111.40 22.53 2.179 ! CPNM 01/10, cmb +CD33A CD315B HDA1R5 34.50 110.10 22.53 2.179 ! TF2M, cmb +CD33A CD315A HDA1R5 34.50 110.10 22.53 2.179 ! CPNM, cmb +OD31A CD315A HDA1R5 34.50 110.10 22.53 2.179 ! CPO1, cmb need test +ND3P2A CD31A CD2O1A 78.50 97.50 ! NTER, PEML +ND3P2A CD31C CD2O1A 78.50 97.50 ! NTER, PEML +ND3P2A CD31A CD2O2A 55.10 104.40 ! NTER, PEML +ND3P2A CD31A CD2O3A 71.90 103.10 ! NTER, PEML +ND3P2A CD31A CD31A 67.80 113.80 ! NTER, PEML +ND3P2A CD31A CD32A 67.80 113.80 ! NTER, PEML +ND3P2A CD31A CD33A 67.80 113.80 ! NTER, PEML +ND3P2A CD31A HDA1C 31.10 106.30 34.90 2.048 ! NTER, PEML +ND3P3A CD31A CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD31C CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD31A CD2O2A 55.10 104.40 ! NTER, PEML +ND3P3A CD31C CD2O2A 55.10 104.40 ! NTER, PEML +ND3P3A CD32C CD2O2A 55.10 104.40 ! NTER, PEML +ND3P3A CD31A CD2O3A 71.90 103.10 ! NTER, PEML +ND3P3A CD31C CD2O3A 71.90 103.10 ! NTER, PEML +ND3P3A CD31A CD31A 67.80 113.80 ! NTER, PEML +ND3P3A CD31C CD31A 67.80 113.80 ! NTER, PEML +ND3P3A CD31A CD32A 67.80 113.80 ! NTER, PEML +ND3P3A CD31C CD32A 67.80 113.80 ! NTER, PEML +ND3P3A CD31C CD32B 67.80 113.80 ! NTER, PEML by analogy GLU, NTER +ND3P3A CD31C CD32C 67.80 113.80 ! NTER, PEML by analogy ASN, NTER +ND3P3A CD31A CD33A 67.80 113.80 ! NTER, PEML +ND3P3A CD31C CD33A 67.80 113.80 ! NTER, PEML +ND3P3A CD31A HDA1C 31.10 106.30 34.90 2.048 ! NTER, PEML +ND3P3A CD31C HDA1C 31.10 106.30 34.90 2.048 ! NTER, PEML +OD31A CD31A CD31A 66.00 113.10 ! THR/PRO2, NTER +OD31A CD31A CD31C 66.00 113.10 ! THR/PRO2 +OD31A CD31A CD32A 59.30 113.10 ! BUO2, 2-butanol +OD31A CD31A CD33A 66.00 113.10 ! PRO2, 2-propanol +OD31A CD31A HDA1A 47.00 104.00 ! PRO2, 2-propanol +CD2O1A CD31A CD31A 42.50 111.30 ! c22, NTER-(X)n-CNEU +CD2O1A CD31A CD32A 42.50 111.30 ! NTER-(X)n-CNEU +CD2O1A CD31A CD33A 42.50 111.30 ! FOR NTER-(X)n-CNEU +CD2O1A CD31A HDA1C 48.90 111.90 ! NTER-(X)n-CNEU +CD2O1A CD31C HDA1C 48.90 111.90 ! NTER-(X)n-CNEU +CD2O2A CD31A CD31A 22.20 116.30 ! NTEZ, PEML +CD2O2A CD31A CD32A 22.20 116.30 ! NTEZ, PEML +CD2O2A CD31A CD33A 22.20 116.30 ! NTER, PEML +CD2O2A CD31A HDA1C 35.30 113.10 39.10 2.257 ! NTER, PEML +CD2O2A CD31C HDA1C 35.30 113.10 39.10 2.257 ! NTER, PEML +CD2O2A CD31C HDA2C 35.30 113.10 39.10 2.257 ! NTER, PEML +CD2O3A CD31A CD31A 55.90 107.50 ! NTER, PEML +CD2O3A CD31A CD32A 55.90 107.50 ! NTER, PEML +CD2O3A CD31A CD33A 25.50 108.20 ! CNEU +CD2O3A CD31A HDA1C 22.90 119.20 10.90 2.121 ! CNEU +CD2O3A CD31C HDA1C 22.90 119.20 10.90 2.121 ! CNEU +CD31A CD31A CD31A 53.35 111.00 8.00 2.561 ! alkane, 3/92 +CD31A CD31A CD32A 58.35 113.50 11.16 2.561 ! glycerol +CD31A CD31A CD33A 53.35 108.50 8.00 2.561 ! alkane, 3/92 +CD31A CD31A HDA1A 34.50 110.10 22.53 2.179 ! alkane, 3/92 +CD31A CD31A HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD31A CD31C HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD31C CD31A CD32A 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31C CD31A CD33A 53.35 108.50 8.00 2.561 ! special case for amides, based on alkane, 3/92 +CD31C CD31A HDA1A 34.50 110.10 22.53 2.179 ! alkane, 3/92 +CD32A CD31A CD32A 58.35 113.50 11.16 2.561 ! glycerol +CD32A CD31A CD33A 53.35 114.00 8.00 2.561 ! alkane 3/2/92 +CD32A CD31A HDA1A 34.50 110.10 22.53 2.179 ! alkane, 3/92 +CD32A CD31A HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD32A CD31C HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD32B CD31C HDA1C 34.50 110.10 22.53 2.179 ! NTER, PEML by analogy GLU, CTER +CD32C CD31C HDA1C 34.50 110.10 22.53 2.179 ! NTER, PEML by analogy ASN, CTER +CD32C CD31A HDA1C 34.50 110.10 22.53 2.179 ! NTER, Isobutane, from HDA1A CD31A CD33A +CD33A CD31A CD33A 55.00 112.00 8.00 2.561 ! IBUT +CD33A CD31A HDA1A 34.50 110.10 22.53 2.179 ! IBUT, isobutane, alkane, 3/92 +CD33A CD31A HDA1C 70.10 116.50 32.50 1.9232 ! ALAD % +CD33A CD31C HDA1C 70.40 117.82 53.70 2.0946 ! ALAD % +ND2A2 CD31C CD2O1A 55.70 103.68 ! ALAD, tau % important for N-Ca-C +ND2A2 CD31C CD2O2A 40.40 112.20 ! CTER, PEML +ND2A2 CD31C CD2O3A 54.60 100.50 ! CT1 +ND2A2 CD31C CD31A 60.60 116.50 ! ALAD % important for N-Ca-Cb 60.60 113.50 ! ALAD +ND2A2 CD31C CD32A 70.00 113.50 ! GLN, c22 % +ND2A2 CD31C CD32B 70.00 113.50 ! GLU, from ND2A2 CD31C CD32A % CHECK THESE +ND2A2 CD31C CD32C 70.00 113.50 ! ASN, c22 % +ND2A2 CD31C CD33A 71.70 118.00 ! ALAD % important for N-Ca-Cb +ND2A2 CD31C HDA1A 34.80 107.70 ! ALAD % +ND3A3 CD31C CD2O1A 20.42 94.79 ! 40.00 112.00 ! PRO +ND3A3 CD31C CD2O2A 20.42 94.79 ! 40.00 112.00 ! PRO +ND3A3 CD31C CD32A 87.40 110.04 ! 70.00 113.00 ! PRO +ND3A3 CD32C CD32A 70.00 113.50 ! PRLD, pyrrolidine, PEML % CHECK THESE ??? +ND3A3 CD31C HDA1A 69.62 109.54 ! 50.00 111.00 ! PRO +OD30C CD31C CD32A 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30C CD31C CD32B 40.00 110.00 ! GLYP, phosphoglycerol lipids +OD30C CD31C CD32C 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30C CD31C CD33A 40.00 110.00 ! EAS, EH 2007 +OD30C CD31C HDA1A 60.00 109.50 ! EAS, Lipid, charmm27 +CD2O1A CD31C CD31A 42.50 111.30 ! ILE, c22 +CD2O1A CD31C CD31C 42.50 111.30 ! ILE, c22 +CD2O1A CD31C CD32A 42.50 111.30 ! LEU/GLN/GLU, c22 +CD2O1A CD31C CD32B 42.50 111.30 ! GLU, from CD2O1A CD31C CD32A +CD2O1A CD31C CD32C 42.50 111.30 ! LEU, c22 +CD2O1A CD31C CD33A 56.90 111.23 ! ALAD % +CD2O1A CD31C HDA1A 27.40 110.87 ! ALAD % important for C-Ca-Ha 58.60 109.90 ! ALAD +CD2O2A CD31C CD31A 30.60 120.70 ! CTER, PEML, Val +CD2O2A CD31C CD32A 30.60 120.70 ! CTER, PEML, Asp +CD2O2A CD31C CD32B 30.60 120.70 ! CTER, PEML, Glu +CD2O2A CD31C CD32C 30.60 120.70 ! CTER, PEML, Asn +CD2O2A CD31C CD33A 30.60 120.70 ! CTER, PEML +CD2O2A CD31C HDA1A 29.70 118.90 5.10 2.137 ! CTER, PEML, ACET +CD2O3A CD31C CD31A 55.90 107.50 ! NTER, PEML +CD2O3A CD31C CD32A 55.90 107.50 ! CNEU +CD2O3A CD31C CD33A 25.50 108.20 ! CNEU +CD2O3A CD31C HDA1A 22.90 119.20 10.90 2.121 ! CNEU +CD31A CD31C HDA1A 34.50 110.10 22.53 2.179 ! special case for amides, based on alkane, 3/92 +CD32A CD31C CD32C 58.35 113.50 11.16 2.5610 ! GLYC, Lipid, alkane +CD32B CD31C CD32C 58.35 113.50 11.16 2.5610 ! GLYP, phosphoglycerol lipids +CD32A CD31C HDA1A 34.50 110.10 22.53 2.1790 ! GLYC, Lipid, alkane +CD32B CD31C HDA1A 34.50 110.10 22.53 2.1790 ! GLU, from CD32A CD31C HDA1A +CD32C CD31C CD33A 58.35 113.50 11.16 2.5610 ! GLYC, Lipid, alkane +CD32C CD31C HDA1A 34.50 110.10 22.53 2.1790 ! GlYC, Lipid, alkane ??? CHECK THIS AGAINST VALUES BELOW +CD33A CD31C HDA1A 70.40 117.82 53.70 2.0946 ! ALAD % +CD325A CD325A CD325A 58.00 106.00 11.16 2.561 ! CPEN 10/17/05 viv +CD325A CD315A CD325A 58.00 106.00 11.16 2.561 ! CPNM 10/17/05 cmb +CD325A CD325A HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +CD315A CD325A HDA2R5 35.00 111.40 22.53 2.179 ! CPNM 10/17/05 cmb +HDA2R5 CD325A HDA2R5 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv +CD315A CD325A CD325A 58.00 109.50 11.16 2.561 ! CPNM 01/10, cmb +CD315A CD33A HDA3A 33.43 110.10 22.53 2.179 ! CPNM, viv; cmb +OD305A CD325B CD325B 45.00 111.10 ! THF, viv 10/21/05 +OD305A CD325B HDA2R5 70.00 107.30 ! THF, viv 10/21/05 +CD315B CD325B CD325B 58.00 109.50 11.16 2.561 ! TF2M 02/09, cmb +CD315B CD325B HDA2R5 35.00 111.40 22.53 2.179 ! TF2M 02/09, cmb +CD325B CD325B CD325B 58.00 109.50 11.16 2.561 ! THF, CSD/NDB survey, viv +CD325B CD325B HDA2R5 35.00 111.40 22.53 2.179 ! CPEN 10/17/05 viv +HDA2R5 CD325B HDA2R5 38.50 106.80 5.40 1.802 ! CPEN 10/17/05 viv +CD326A CD326A CD326A 58.35 113.60 11.16 2.561 ! CHEX, from alkane CD32A, 9/09, cmb +CD326A CD316A CD33A 53.35 114.00 8.00 2.561 ! CHXM, from alkane 3/2/92, cmb 12/09 +CD316A CD33A HDA3A 33.43 110.10 22.53 2.179 ! CHXM, from alkane, 4/98, 12/09, cmb +CD33A CD316A HDA1A 34.50 110.10 22.53 2.179 ! CHXM, from, IBUT, 3/92, 12/09, cmb +CD326A CD316A CD326A 58.35 113.60 11.16 2.561 ! CHXM, from alkane CD32A, 12/09, cmb +CD316A CD326A CD326A 58.35 113.60 11.16 2.561 ! CHXM, from alkane CD32A, 12/09, cmb +CD326A CD316A HDA1A 26.50 110.10 22.53 2.179 ! CHXM, from alkane CD32A, 12/09, cmb +CD316A CD326A HDA2A 26.50 110.10 22.53 2.179 ! CHXM, from alkane CD32A, 9/09, cmb +CD326A CD326A HDA2A 26.50 110.10 22.53 2.179 ! CHEX, from alkane CD32A, 9/09, cmb +HDA2A CD326A HDA2A 35.50 109.00 5.40 1.802 ! CHEX, from alkane CD32A, 9/09, cmb +OD306A CD326B CD326B 45.00 111.50 ! THP, viv +OD306A CD326B HDA2E 45.00 109.50 ! THP, sng +CD326B CD326B CD326B 58.35 112.00 11.16 2.561 ! cyclohexane, sng +CD326B CD326B HDA2E 34.50 110.10 22.53 2.179 ! cyclohexane, sng +HDA2E CD326B HDA2E 35.50 109.00 5.40 1.802 ! THP viv +ND2P1A CD32A CD32A 74.70 116.10 ! ARG, from GEOM OPT of GUAN (PEML) +ND2P1A CD32A HDA2A 51.50 107.50 ! ARG, c22 +ND3A3 CD32A CD32A 70.00 113.00 ! PRO +ND3A3 CD32A HDA2A 50.00 111.00 ! PRO +ND3P2A CD31C CD32A 67.70 113.00 ! CHOL, qm EH 2007, ammonium cations +ND3P2A CD32A CD32A 67.70 113.00 ! CHOL, qm EH 2007, ammonium cations +ND3P2A CD32A CD33A 67.70 113.00 ! NC5, qm EH 2007, ammonium cations +ND3P2A CD31C HDA1C 40.00 109.50 27.00 2.1300 ! NC4, charmm27, ammonium cations +ND3P2A CD32A HDA2C 40.00 109.50 27.00 2.1300 ! NC4, charmm27, ammonium cations +ND3P3A CD32A CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD32C CD2O1A 78.50 97.50 ! NTER, PEML +ND3P3A CD32A CD32A 67.70 113.00 ! ETAM, qm EH 2007, ammonium cations +ND3P3A CD32C CD32A 67.70 113.00 ! ETAM, qm EH 2007, ammonium cations +ND3P3A CD32A CD33A 67.70 113.00 ! NH5, qm EH 2007, ammonium cations +ND3P3A CD32A HDA2A 40.00 109.50 27.00 2.1300 ! NC1, charmm27 +ND3P3A CD32A HDA2C 40.00 109.50 27.00 2.1300 ! NC1, charmm27 +ND3P3A CD32C HDA2C 40.00 109.50 27.00 2.1300 ! NC1, charmm27 +OD30A CD32A CD32A 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32A CD33A 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32A HDA2A 60.00 109.50 ! DMP, dimethylphosphate, alex +OD30B CD32A CD31C 75.70 110.10 ! DMP, Lipid, charmm27, need work** +OD30B CD32B CD31C 75.70 110.10 ! GLYP, phosphoglycerol lipids +OD30B CD32A CD32A 75.70 110.10 ! DMP, Lipid, charmm27, need work** +OD30B CD32A HDA2A 60.00 109.50 ! DMP, charmm27 +OD30B CD32B HDA2A 60.00 109.50 ! GLYP, phosphoglycerol lipids +OD31A CD32A CD31C 66.00 112.50 ! SER/PRO1 +OD31A CD32A CD32A 66.00 112.50 ! ETAM +OD31A CD32A CD33A 66.00 112.50 ! ETOH, ethanol +OD31A CD32A HDA2A 54.00 111.50 ! ETOH, ethanol +OD31B CD32A CD32A 66.00 112.50 ! PRO1, 1-propanol +OD31B CD32A HDA2A 54.00 111.50 ! PRO1, 1-propanol +SD30A CD32A CD32A 65.00 113.20 ! EMS, Met +SD30A CD32A CD33A 65.00 113.20 ! EMS +SD30A CD32A HDA2A 30.10 109.80 ! EMS +SD30B CD32A CD31C 58.00 112.50 ! DMDS, c22, Disulfide patch +SD30B CD32A HDA2A 42.70 108.30 ! DMDS, Disulfide patch +SD31B CD32A CD31C 43.00 113.20 ! PRSH +SD31B CD32A CD32A 43.00 113.20 ! PRSH +SD31B CD32A CD33A 43.00 113.20 ! ETSH +SD31B CD32A HDA2A 46.10 106.30 ! ETSH +CD2O1A CD32A HDA2C 48.90 111.90 ! NTER-(X)n-CNEU +CD2O1A CD32C HDA2C 48.90 111.90 ! NTER-(X)n-CNEU +CD2O2A CD32A CD31C 22.20 116.30 ! NTEZ, PEML +CD2O2A CD32A CD32A 30.60 120.70 ! CTER, PEML, Glu +CD2O2A CD32A CD32B 30.60 120.70 ! GLU, from CD2O2A CD32A CD32B +CD2O2A CD32A HDA2A 29.70 118.90 5.10 2.137 ! CTER, PEML, Asp +CD2R5A CD32A CD31C 58.35 113.00 ! HSD, c22 +CD2R5A CD32A HDA2A 33.43 109.50 ! HSD, 4MIM, 4-methyl-imidazole +CD2R5C CD32A CD31C 58.35 113.00 ! TRP, c22 +CD2R5C CD32A HDA2A 49.30 107.50 ! INDM, methyl-indole, Trp +CD2R5D CD32A CD31C 58.35 113.00 ! HSP, c22 +CD2R5D CD32A HDA2A 33.43 109.50 ! HSP, 4MIM, 4-methyl-imidazole +CD2R6A CD32A CD31C 51.80 107.50 ! PHE, c22 +CD2R6A CD32A HDA2A 49.30 107.50 ! PHE/TOLU +CD30A CD32A CD32A 58.35 113.50 11.16 2.561 ! glycerol ? need check +CD30A CD32A CD33A 58.35 113.50 11.16 2.561 ! glycerol ? need check +CD30A CD32A HDA2A 26.50 110.10 22.53 2.179 ! alkane, 4/98 ? need check +CD31A CD32A CD31A 58.35 113.50 11.16 2.561 ! glycerol +CD31A CD32A CD31C 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31A CD32A CD32A 58.35 113.50 11.16 2.561 ! glycerol +CD31A CD32A CD32C 58.35 113.50 11.16 2.561 ! NTER +CD31A CD32A CD33A 58.35 113.50 11.16 2.561 ! glycerol +CD31A CD32A HDA2A 26.50 110.10 22.53 2.179 ! alkane, 4/98 +CD31C CD32A CD32A 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31C CD32B CD32A 58.35 113.50 11.16 2.561 ! GLU, from CD31C CD32A CD32A +CD31C CD32B CD32C 58.35 113.50 11.16 2.561 ! GLUP, from CD31C CD32A CD32A +CD31C CD32A CD32C 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31C CD32A CD33A 58.35 113.50 11.16 2.561 ! special case for amides, based on glycerol +CD31C CD32A HDA2A 34.60 110.10 22.53 2.1790 ! MBU, alkane +CD31C CD32B HDA2A 34.60 110.10 22.53 2.1790 ! GLU, from CD31C CD32A HDA2A +CD32A CD32A CD32A 58.35 113.60 11.16 2.561 ! alkane, 3/92 +CD32A CD32A CD32C 58.35 113.60 11.16 2.5610 ! GLYC, Lipid, alkane +CD32A CD32A CD32E 58.35 113.60 11.16 2.561 ! ethers +CD32A CD32A CD33A 58.00 115.00 8.00 2.561 ! alkane, 3/92 +CD32A CD32A HDA2A 26.50 110.10 22.53 2.179 ! alkane, 4/98 +CD32A CD32B HDA2A 26.50 110.10 22.53 2.179 ! GLU, from CD32A CD32A HDA2A +CD32B CD32A HDA2A 26.50 110.10 22.53 2.179 ! GLU, from CD32A CD32A HDA2A +CD32B CD32C HDA2A 26.50 110.10 22.53 2.179 ! GLUP, from CD32A CD32A HDA2A +CD32A CD32A HDA2C 26.50 110.10 22.53 2.179 ! LYS, alkane, 4/98 +CD32C CD32A CD33A 58.00 115.00 8.00 2.5610 ! MBU, alkane +CD32C CD32A HDA2A 34.60 110.10 22.53 2.1790 ! MBU, alkane +CD32C CD32B HDA2A 34.60 110.10 22.53 2.1790 ! MBU, alkane, GLUP +CD32E CD32A CD33A 58.00 115.00 8.00 2.561 ! ethers +CD32E CD32A HDA2A 26.50 110.10 22.53 2.179 ! ether +CD33A CD32A CD33A 53.35 114.00 8.00 2.561 ! alkane 3/92 +CD33A CD32A HDA2A 34.60 110.10 22.53 2.179 ! alkane, 4/98 +CD33A CD32A HDA2C 26.50 110.10 22.53 2.1790 ! NC5, alkane, ammonium cations +HDA2A CD32A HDA2A 35.50 109.00 5.40 1.802 ! alkane, 3/92 +HDA2A CD32B HDA2A 35.50 109.00 5.40 1.802 ! GLU, from HDA2A CD32A HDA2A +HDA2C CD32A HDA2C 24.00 109.50 28.00 1.7670 ! NC4, charmm27 +HDA2C CD32C HDA2C 24.00 109.50 28.00 1.7670 ! NC4, charmm27 +ND2A2 CD32C CD2O1A 58.55 100.46 ! GLYD, tau, needs to be checked +ND2A2 CD32C CD2O2A 40.40 112.20 ! CTER, terminal Gly +ND2A2 CD32C CD2O3A 54.60 100.50 ! CNEU +ND2A2 CD32C HDA2A 42.50 111.30 ! GLYD +ND3A3 CD32C HDA2A 42.50 111.30 ! PRLD, pyrrolidine, PEML +OD30C CD32C CD31C 40.00 110.00 ! EAS, Lipid, EH 2007 +OD30C CD32C CD33A 40.00 110.00 ! EAS, EH 2007 +OD30C CD32C HDA2A 60.00 109.50 ! MAS, charmm27 +CD2O1A CD32C CD31C 42.50 111.30 ! ASN, c22 +CD2O1A CD32C CD32A 42.50 111.30 ! GLN, c22 +CD2O1A CD32C HDA2A 42.50 111.30 ! GLYD +CD2O2A CD32C HDA2A 29.70 118.90 5.10 2.137 ! CTER, PEML, ACET, terminal Gly +CD2O3A CD32C CD31C 52.00 108.00 ! MBU, alkane, ASPP +CD2O3A CD31C CD32B 52.00 108.00 ! PEML by analogy GLU, CNEU +CD2O3A CD31C CD32C 52.00 108.00 ! PEML by analogy ASN, CNEU +CD2O3A CD32C CD32B 52.00 108.00 ! MBU, alkane, GLUP +!revert_lipid +!CD2O3A CD32C CD32A 52.00 108.00 ! MBU, alkane +!CD2O3A CD32C CD33A 52.00 108.00 ! MPO, alkane +!CD2O3A CD32C HDA2A 33.00 109.50 30.00 2.1630 ! MPO, charmm27 +CD31C CD32C HDA2A 26.50 110.10 22.53 2.1790 ! GLYC, Lipid, alkane +CD32A CD32C HDA2A 26.50 110.10 22.53 2.1790 ! MBU, alkane +CD33A CD32C HDA2A 34.60 110.10 22.53 2.1790 ! MPO, alkane +HDA2A CD32C HDA2A 35.50 109.00 5.40 1.8020 ! MPO, alkane +OD30A CD32E CD32A 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32E CD32E 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32E CD33A 45.00 111.50 ! DEET, diethylether, alex +OD30A CD32E HDA2E 60.00 109.50 ! DMP, ethers +CD32A CD32E HDA2E 26.50 110.10 22.53 2.179 ! ether +CD32E CD32E HDA2E 26.50 110.10 22.53 2.179 ! ether +CD33A CD32E HDA2E 34.60 110.10 22.53 2.179 ! ether +HDA2E CD32E HDA2E 35.50 109.00 5.40 1.802 ! ethers +ND2P1A CD33A HDA3A 51.50 107.50 ! GUAN, c22 +ND2R5D CD33A HDA3A 33.43 107.00 ! ADE, cmb 04/10 +ND2R6C CD33A HDA3A 33.43 104.00 ! CYT, cmb 04/10 +ND3P2A CD33A HDA3C 40.00 109.50 27.00 2.1300 ! NC4, charmm27, ammonium cations +ND3P3A CD33A HDA3C 40.00 109.50 27.00 2.1300 ! NC1, charmm27, ammonium cations +OD30A CD33A HDA3A 60.00 109.50 ! DMP, dimethylphosphate, alex +OD30B CD33A HDA3A 60.00 109.50 ! DMP, charmm27 +SD30A CD33A HDA3A 41.30 109.00 ! EMS +SD30B CD33A HDA3A 42.70 108.30 ! DMDS +SD31A CD33A HDA3A 40.00 108.69 ! MESH +CD2O2A CD33A HDA3A 27.70 107.50 25.30 2.1670 ! ACET, PEML +CD2R5A CD33A HDA3A 33.43 109.50 ! 4MIM, 4-methyl-imidazole +CD2R5C CD33A HDA3A 49.30 107.50 ! INDM, methyl-indole +CD2R6A CD33A HDA3A 49.30 107.50 ! TOLU, toluene +CD2R6J CD33A HDA3A 49.30 107.50 ! TOLU, toluene, THY, jal +CD30A CD33A HDA3A 33.43 110.10 22.53 2.179 ! alkane, 4/98 ? need check +CD315B CD33A HDA3A 33.43 110.10 22.53 2.179 ! TF2M, viv; cmb +CD31A CD33A HDA3A 33.43 110.10 22.53 2.179 ! alkane, 4/98 +CD31C CD33A HDA3A 34.60 110.10 22.53 2.1790 ! MPO, alkane +CD32A CD33A HDA3A 34.60 111.50 22.53 2.179 ! alkane, 4/98 +CD32C CD33A HDA3A 34.60 110.10 22.53 2.1790 ! MPO, alkane +CD32E CD33A HDA3A 34.60 111.50 22.53 2.179 ! ether +CD33A CD33A HDA3A 37.50 110.10 22.53 2.179 ! alkane, 4/98 +HDA3A CD33A HDA3A 35.50 108.40 5.40 1.802 ! alkane, 3/92 +HDA3C CD33A HDA3C 24.00 109.50 28.00 1.7670 ! NC4, charmm27, ammonium cations +OD31A CD33B HDA3B 61.00 108.89 ! MEOH, methanol +HDA3B CD33B HDA3B 35.50 108.40 5.40 1.802 ! alkane, 3/92, special for MEOH, methanol +ND2A2 CD33C HDA3A 85.60 126.43 ! NMA+ALAD % +ND2A3 CD33C HDA3A 51.50 109.50 ! DMA % +OD30D CD33C HDA3A 60.00 109.50 ! MP_1 +OD30B CD33C HDA3A 60.00 109.50 ! DMP, cmb, nucleic acids +OD30BR CD33C HDA3A 60.00 109.50 ! DMP, nucleic acids, copied for RNA, jal +OD30C CD33C HDA3A 60.00 109.50 ! MAS, charmm27 +CD2O1A CD33C HDA3A 49.00 107.87 ! NMA+ALAD % +HDA3A CD33C HDA3A 35.50 108.40 5.40 1.8020 ! MAS, alkane +OD30A CD33E HDA3A 60.00 109.50 ! DMP, ethers +HDA3A CD33E HDA3A 35.50 108.40 5.40 1.802 ! ethers +CD2R6A CD32A CD31A 51.80 107.50 ! PHE, c22 !!PEML added to allow NTER patch on TYR +CD2R6J CD32A CD31A 51.80 107.50 ! PHE, c22 !!PEML added to allow NTER patch on TYR +!alkenes +CD32A CD2C1A HD2C1A 45.66 117.891 ! BTE1, PTE1, 2BTE, 2PTE, HXE1, 2HEX; pc 06/2022 +CD33A CD2C1A HD2C1A 47.71 115.41 ! PRPE, 2BTE +CD2C1A CD2C1A CD32A 44.33 123.82 ! 2PTE,2HEX,3HEX;pc 10/2022 +CD2C1A CD2C1A CD33A 50.04 124.53 ! 2BTE, 2PTE; pc 06/2022 +CD2C1A CD32A CD32A 64.33 112.237 ! PTE1, HXE1, 2HEX ; pc 06/2022 +CD2C1A CD32A CD33A 33.53 111.544 ! BTE1, 2BTE; pc 06/2022 +CD2C1A CD33A HDA3A 49.02 110.95 ! 2BTE ; pc 06/2022 +CD2C1A CD32A HDA2A 47.03 110.646 ! BTE1, PTE1, 2BTE, 2PTE, HXE1, 2HEX; pc 06/2022 +CD2C1A CD2C1A HD2C1A 32.03 121.14 ! 2BTE , 2PTE, 2HEX ; pc 06/2022 +CD2C1A CD2C1B HD2C1B 32.03 121.14 ! PRPE, BTE1, PTE1,HXE1 +CD2C1B CD2C1B HD2C1B 32.03 121.14 ! ETHE ; pc 06/2022 +CD2C1B CD2C1A CD33A 45.04 124.63 ! PRPE ; pc 06/2022 +CD2C1B CD2C1A HD2C1A 35.03 118.29 ! PRPE, BTE1, PTE1, HXE1, PRPE ; pc 06/2022 +CD2C1B CD2C1A CD32A 64.00 123.82 ! BTE1 PTE1, HTE1, HXE1; pc 06/2022 +HD2C1B CD2C1B HD2C1B 45.66 117.89 ! ETHE, PRPE, BTE1, PTE1,HXE1; pc 06/2022 +CD2C1A CD2C1A CD326A 40.33 117.96 ! CHXE, 06/2022 +CD326A CD2C1A HD2C1A 45.66 117.89 ! CHXE, 06/2022 +CD2C1A CD326A CD326A 45.50 111.5 30.13 2.4000 !CHXE; pc 06/2022 +CD2C1A CD326A HDA2A 43.00 111.00 ! CHXE;06/2022 +!alkenes end +!carbonyls +CD2O1D CD33C HDA3A 38.70 109.30 ! +OD2C1D CD2O1D CD33C 63.60 121.81 ! +CD33C CD2O1D CD33C 44.50 116.38 ! acetone 44.5 116.44; +OD2C1D CD2O1D CD32C 60.60 121.19 ! +CD33C CD2O1D CD32C 47.60 117.00 ! +CD2O1D CD32C CD33A 55.40 110.90 ! 2-butanone 55.4 111.30; 3-pentanone 110.50; +CD2O1D CD32C HDA2A 39.00 107.77 ! +CD2O1D CD32C CD32A 57.50 110.20 ! 2-petanone 57.5 110.20; +CD32C CD2O1D CD32C 52.50 117.80 ! 3-pentanone 52.5 117.8; +OD2C1D CD2O1C HDP1C 55.5 118.00 ! +OD2C1C CD2O1C HDP1C 55.5 118.00 ! +HDP1C CD2O1C CD33C 20.00 115.30 ! ethanal 20.0 115.370 +CD2O1C CD33C HDA3A 38.70 109.30 ! +OD2C1C CD2O1C CD33C 63.60 123.81 ! +OD2C1C CD2O1C CD32C 60.60 121.19 ! +OD2C1C CD2O1C CD31C 60.60 121.19 ! +CD2O1C CD32C CD33A 55.40 110.90 ! 2-butanone 55.4 111.30; 3-pentanone 110.50; +CD2O1C CD32C HDA2A 39.00 107.77 ! +CD2O1C CD32C CD32A 57.50 110.20 ! 2-petanone 57.5 110.20; +CD2O1C CD31C CD33A 55.40 110.90 ! 2-butanone 55.4 111.30; 3-pentanone 110.50; +CD2O1C CD31C HDA1A 39.00 107.77 ! +CD33A CD31C CD33A 58.35 113.50 11.16 2.561 ! double check +HDP1C CD2O1C CD32C 30.0 115.22 ! propanal 30.0 115.22 +HDP1C CD2O1C CD31C 30.0 115.22 ! propanal 30.0 115.22 +HDA2A CD32F CD2O1D 26.50 110.10 22.53 2.179 ! from MRIBOL HDA2A CD32F CD31G +OD31E CD32F CD2O1D 66.00 111.00 ! from MRIBOL OD31E CD32F CD31G +CD32F CD2O1D OD2C1D 63.60 121.81 ! from ACO CD33C CD2O1D OD2C1D +CD32F CD2O1D CD31G 44.50 116.38 ! from ACO CD33C CD2O1D CD33C +OD2C1D CD2O1D CD31G 63.60 121.81 ! from ACO OD2C1D CD2O1D CD33C +CD2O1D CD31G CD31G 55.40 110.90 ! from BTON CD2O1D CD32C CD33A +CD2O1D CD31G HDA1A 39.00 107.77 ! from BTON CD2O1D CD32C HDA2A +CD2O1D CD31G OD31E 39.00 107.77 ! from BTON CD2O1D CD32C HDA2A +HDP1C CD2O1C CD31G 30.0 115.22 ! +OD2C1C CD2O1C CD31G 30.0 115.22 ! +CD2O1C CD31G OD31E 39.00 107.77 ! +CD2O1C CD31G HDA1A 39.00 107.77 ! from PALD CD2O1C CD32C HDA2A +CD2O1C CD31G CD31G 58.35 113.50 11.16 2.561 ! +!carbonyls end +!! BGUAN +ND2P1A CD32A HDA2C 51.50 107.50 ! GUAN, c22 40.00 109.50 27.00 2.1300 ! NC4, charmm27, ammonium cations +! for N-ethylacetamide, jal +CD33A CD32C ND2A2 71.70 118.00 ! copied from ND2A2-CD31C-CD33A (ALAD), needs opt +! for N-propylacetamide, jal +ND2A2 CD32C CD32A 70.00 113.50 ! copied from ND2A2-CD31C-CD32A (GLN, c22), needs opt +!molecular anions, a&a +OD2C2B SD1A OD2C2B 60.00 115.35 ! SO4, a&a +OD2C2B SD1A OD30B 90.00 98.44 ! MSO4, a&a +SD1A OD30B CD33C 40.00 109.00 ! MSO4, a&a +OD30E CD33A HDA3A 61.00 117.20 ! MEO, a&a +OD30E CD32A CD33A 66.00 112.50 ! ETO, a&a +OD30E CD32A HDA2A 54.00 111.50 ! ETO, a&a +SD1A ND2A2 HDP1A 48.00 118.00 ! NMSM, a&a +CD33C ND2A2 SD1A 40.00 109.00 ! NMSM, a&a +ND2A2 CD32C CD33C 50.00 109.00 ! NESM, a&a +OD2C2B SD1A ND2A2 50.00 113.00 ! NMSM, NESM, a&a +CD32C ND2A2 SD1A 40.00 109.00 ! NESM, a&a +CD32C CD33C HDA3A 34.60 110.10 22.53 2.1790 ! NESM, a&a +HDA2A CD32C CD33C 34.60 110.10 22.53 2.1790 ! NESM, a&a +OD2C2B SD1A CD33C 60.00 103.55 ! MSNA, a&a +SD1A CD33C HDA3A 35.00 108.80 ! MSNA, a&a + +DIHEDRALS +!atom types Kchi n delta +!================================================ +! +!Please follow these conventions when fitting torsion parameters +!1) use positive force constants in all cases (switch the phase...) +! (vary phase during fitting and keep force constants positive) +!2) maintain the phase at 0 or 180 if possiple. perform initial +! fitting with this contraint and, if necessary, only then +! vary the phases during fitting. note that if the phases +! are NOT 0 or 180 the parameters are NOT transferable across +! stereoisomers +!3) refit with only individual multiplicities of 1 through 6 +!4) maintain the number of significant figures used below +! +HDP1A ND2A1 CD2O1A OD2C1A 2.000 2 180.00 ! ACEM +HDP1A ND2A1 CD2O1A CD31C 2.000 2 180.00 ! CT2/ACEM +HDP1A ND2A1 CD2O1A CD32C 2.000 2 180.00 ! ASN, ACEM +HDP1A ND2A1 CD2O1A CD33C 2.000 2 180.00 ! ACEM +HDP1A ND2A1 CD2O1C OD2C1D 3.000 2 180.00 ! FORM, fylin +HDP1A ND2A1 CD2O1C HDP1C 0.900 2 180.00 ! FORM, fylin +HDP1A ND2B1 CD2R6C ND2R6C 1.400 2 180.00 ! GUA, cmb 04/10 +CD31C ND2A2 CD2O1A OD2C1A 6.390 2 180.00 ! ALAD omega left % +CD31C ND2A2 CD2O1A OD2C1A 0.680 3 0.00 ! ALAD omega left % +CD31C ND2A2 CD2O1A CD31A 1.700 1 0.00 ! NTER, from NMA +CD31C ND2A2 CD2O1A CD31A 2.000 2 180.00 ! NTER, from NMA +CD31C ND2A2 CD2O1A CD31C 0.820 1 0.00 ! ALAD omega +CD31C ND2A2 CD2O1A CD31C 3.000 2 180.00 ! ALAD omega +CD31C ND2A2 CD2O1A CD32C 0.820 1 0.00 ! GLYD omega right +CD31C ND2A2 CD2O1A CD32C 3.000 2 180.00 ! GLYD omega right +CD31C ND2A2 CD2O1A CD33C 0.010 1 0.00 ! ALAD acetylated N-terminus omega left % +CD31C ND2A2 CD2O1A CD33C 1.880 2 180.00 ! ALAD acetylated N-terminus omega left % +CD31C ND2A2 CD2O1A CD33C 0.480 3 0.00 ! ALAD acetylated N-terminus omega left % +CD31C ND2A2 CD2O1A CD33C 0.530 4 0.00 ! ALAD acetylated N-terminus omega left % +CD32C ND2A2 CD2O1A OD2C1A 0.820 1 180.00 ! GLYD omega right +CD32C ND2A2 CD2O1A OD2C1A 3.000 2 180.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD31C 0.820 1 0.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD31C 3.000 2 180.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD32A 1.000 1 0.00 ! GLYD +CD32C ND2A2 CD2O1A CD32A 2.500 2 180.00 ! GLYD +CD32C ND2A2 CD2O1A CD32C 0.820 1 0.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD32C 3.000 2 180.00 ! GLYD omega right +CD32C ND2A2 CD2O1A CD33A 1.000 1 0.00 ! GLYD/NMA +CD32C ND2A2 CD2O1A CD33A 2.500 2 180.00 ! GLYD/NMA +CD32C ND2A2 CD2O1A CD33C 0.820 1 0.00 ! GLYD acetylated N-terminus omega left +CD32C ND2A2 CD2O1A CD33C 3.000 2 180.00 ! GLYD acetylated N-terminus omega left +CD33C ND2A2 CD2O1A OD2C1A 0.820 1 180.00 ! NMA/ALAD N-acetyl C-terminus omega right % +CD33C ND2A2 CD2O1A OD2C1A 3.000 2 180.00 ! NMA/ALAD N-acetyl C-terminus omega right % +CD33C ND2A2 CD2O1A CD31A 2.000 2 180.00 ! NTER, from NMA +CD33C ND2A2 CD2O1A CD31C 0.670 1 0.00 ! ALAD N-acetyl C-terminus omega right % +CD33C ND2A2 CD2O1A CD31C 3.460 2 180.00 ! ALAD N-acetyl C-terminus omega right % +CD33C ND2A2 CD2O1A CD32A 1.000 1 0.00 ! GLYD/NMA +CD33C ND2A2 CD2O1A CD32A 2.500 2 180.00 ! GLYD/NMA +CD33C ND2A2 CD2O1A CD32C 0.820 1 0.00 ! GLYD omega right +CD33C ND2A2 CD2O1A CD32C 3.000 2 180.00 ! GLYD omega right +CD33C ND2A2 CD2O1A CD33C 0.820 1 0.00 ! NMA % +CD33C ND2A2 CD2O1A CD33C 3.000 2 180.00 ! NMA +HDP1A ND2A2 CD2O1A OD2C1A 0.000 2 180.00 ! ALAD peptide bond omega right +HDP1A ND2A2 CD2O1A CD31A 3.900 2 180.00 ! NTER +HDP1A ND2A2 CD2O1A CD31C 0.000 2 180.00 ! ALAD omega right +HDP1A ND2A2 CD2O1A CD32A 3.900 2 180.00 ! GLYP/NTER +HDP1A ND2A2 CD2O1A CD32C 0.000 2 180.00 ! GLYD omega right +HDP1A ND2A2 CD2O1A CD33C 0.000 2 180.00 ! NMA/acetylated N-terminus +CD2O1A ND2A2 CD31C CD2O1A 0.000 3 180.00 ! ALAD, phi, cmap +CD2O1A ND2A2 CD31C CD2O2A 4.000 1 0.00 ! CTER, PEML, pseudo-phi from ACE-CTER % +CD2O1A ND2A2 CD31C CD2O2A 2.500 2 180.00 ! CTER, PEML, pseudo-phi from ACE-CTER %k +CD2O1A ND2A2 CD31C CD2O3A 0.300 1 0.00 ! CNEU, PEML pseudo-phi +CD2O1A ND2A2 CD31C CD2O3A 0.000 2 180.00 ! CNEU, PEML pseudo-phi +CD2O1A ND2A2 CD31C CD31A 1.800 1 0.00 ! ILE/VAL, c22 +CD2O1A ND2A2 CD31C CD32A 1.800 1 0.00 ! GLN, c22 +CD2O1A ND2A2 CD31C CD32B 1.800 1 0.00 ! GLU, from CD2O1A ND2A2 CD31C CD32A +CD2O1A ND2A2 CD31C CD32C 1.800 1 0.00 ! ASN, c22 +CD2O1A ND2A2 CD31C CD33A 0.000 1 0.00 ! ALAD, phi, cmap +CD2O1A ND2A2 CD31C HDA1A 0.200 3 0.00 ! ALAD, phi, cmap +HDP1A ND2A2 CD31C CD2O1A 0.000 1 0.00 ! ALAD, phi, cmap +HDP1A ND2A2 CD31C CD2O2A 2.500 3 0.00 ! CTER PEML +HDP1A ND2A2 CD31C CD2O3A 0.000 3 0.00 ! CNEU, PEML pseudo-phi +HDP1A ND2A2 CD31C CD31A 0.200 3 0.00 ! ILE/VAL, alkanes +HDP1A ND2A2 CD31C CD32A 0.200 3 0.00 ! GLN, c22 +HDP1A ND2A2 CD31C CD32B 0.200 3 0.00 ! GLU, from HDP1A ND2A2 CD31C CD32A +HDP1A ND2A2 CD31C CD32C 0.000 1 0.00 ! ASN, c22 +HDP1A ND2A2 CD31C CD33A 0.000 1 0.00 ! ALAD, phi, cmap +HDP1A ND2A2 CD31C HDA1A 0.160 3 0.00 ! ALAD, phi, cmap +CD2O1A ND2A2 CD32C CD2O1A 0.000 3 180.00 ! GLYD, phi, cmap +CD2O1A ND2A2 CD32C CD2O2A 3.000 1 0.00 ! CTER, PEML, GLY +CD2O1A ND2A2 CD32C CD2O2A 2.000 2 180.00 ! CTER, PEML, GLY +CD2O1A ND2A2 CD32C CD2O3A 3.500 1 0.00 ! CNEU, PEML, gly +CD2O1A ND2A2 CD32C HDA2A 0.200 3 0.00 ! GLYD +HDP1A ND2A2 CD32C CD2O1A 0.000 1 0.00 ! GLYD, phi, cmap +HDP1A ND2A2 CD32C CD2O2A 2.500 3 0.00 ! CTER PEML, GLY +HDP1A ND2A2 CD32C CD2O3A 2.500 3 0.00 ! GLYP/CTER PEML +HDP1A ND2A2 CD32C HDA2A 0.160 3 0.00 ! GLYD, phi, cmap +CD2O1A ND2A2 CD33C HDA3A 0.200 3 0.00 ! NMA +HDP1A ND2A2 CD33C HDA3A 0.160 3 0.00 ! NMA +HDP1A ND3A3 CD32C HDA2A 0.160 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ?? +HDP1A ND3A2 CD31C HDA1A 0.185 3 0.00 ! NNEU, based on HDA2A CD32A ND3A2 HDP1A, eam1 +HDP1A ND3A2 CD32C HDA2A 0.185 3 0.00 ! NNEU-Gly, based on HDA2A CD32A ND3A2 HDP1A, eam1 +HDP1A ND3A2 CD31C CD31A 0.290 3 0.00 ! NNEU, based on CD32A CD32A ND3A2 HDP1A, pam1 +HDP1A ND3A2 CD31C CD32A 0.290 3 0.00 ! NNEU, based on CD32A CD32A ND3A2 HDP1A, pam1 +HDP1A ND3A2 CD31C CD32B 0.290 3 0.00 ! NNEU, based on CD32A CD32A ND3A2 HDP1A, pam1 +HDP1A ND3A2 CD31C CD32C 0.290 3 0.00 ! NNEU, based on CD32A CD32A ND3A2 HDP1A, pam1 +HDP1A ND3A2 CD31C CD33A 0.290 3 0.00 ! NNEU, based on CD32A CD32A ND3A2 HDP1A, pam1 +HDP1A ND3A2 CD31C CD2O1A 0.290 3 0.00 ! NNEU, based on CD32A CD32A ND3A2 HDP1A, pam1 +HDP1A ND3A2 CD32C CD2O1A 0.290 3 0.00 ! NNEU-Gly, based on CD32A CD32A ND3A2 HDP1A, pam1 +ND2A2 CD2O1A CD31C ND3A2 0.300 1 180.00 ! NNEU, based on ND2A2 CD2O1A CD31C ND3P3A, NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31C ND3A2 2.400 2 180.00 ! NNEU, based on ND2A2 CD2O1A CD31C ND3P3A, NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31C ND3A2 0.300 1 0.00 ! NNEU, based on OD2C1A CD2O1A CD31C ND3P3A, NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31C ND3A2 2.400 2 180.00 ! NNEU, based on OD2C1A CD2O1A CD31C ND3P3A, NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD32C ND3A2 0.300 1 180.00 ! NNEU-Gly, based on ND2A2 CD2O1A CD31C ND3P3A, NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD32C ND3A2 2.400 2 180.00 ! NNEU-Gly, based on ND2A2 CD2O1A CD31C ND3P3A, NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD32C ND3A2 0.300 1 0.00 ! NNEU-Gly, based on OD2C1A CD2O1A CD31C ND3P3A, NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD32C ND3A2 2.400 2 180.00 ! NNEU-Gly, based on OD2C1A CD2O1A CD31C ND3P3A, NTER-CT3 pseud-psi %% +ND3A2 CD31C CD31A HDA1A 0.000 1 0.00 ! NNEU, based on ND3P3A CD31C CD31A HDA1A, NTER +ND3A2 CD31C CD32A HDA2A 0.000 1 0.00 ! NNEU, based on ND3P3A CD31C CD31A HDA1A, NTER +ND3A2 CD31C CD32B HDA2A 0.000 1 0.00 ! NNEU, based on ND3P3A CD31C CD31A HDA1A, NTER +ND3A2 CD31C CD32C HDA2A 0.000 1 0.00 ! NNEU, based on ND3P3A CD31C CD31A HDA1A, NTER +ND3A2 CD31C CD33A HDA3A 0.000 1 0.00 ! NNEU, based on ND3P3A CD31C CD31A HDA1A, NTER +ND3A2 CD31C CD31A CD33A 0.550 1 180.00 ! NNEU, based on ND3P3A CD31C CD31A CD33A, ILE/VAL, chi1, Xiao, NTER +ND3A2 CD31C CD31A CD33A 0.230 2 0.00 ! NNEU, based on ND3P3A CD31C CD31A CD33A, ILE/VAL, chi1, Xiao, NTER +ND3A2 CD31C CD31A CD33A 0.540 3 0.00 ! NNEU, based on ND3P3A CD31C CD31A CD33A, ILE/VAL, chi1, Xiao, NTER +ND3A2 CD31C CD32A CD32C 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A CD32C, NTER +ND3A2 CD31C CD32A CD2R5A 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A CD2R5A, NTER, PEML by analogy for HSD +ND3A2 CD31C CD32A CD2R5C 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A CD2R5C, NTER, PEML by analogy for TRP +ND3A2 CD31C CD32A CD2R5D 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A CD2R5D, NTER, PEML by analogy for HSP +ND3A2 CD31C CD32A CD2R6A 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A CD2R6A, NTER, PEML by analogy for PHE +ND3A2 CD31C CD31A CD32A 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD31A CD32A, NTER, PEML by analogy for ILE +ND3A2 CD31C CD32A CD31A 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A CD31A, NTER, PEML by analogy for LEU +ND3A2 CD31C CD32A CD32A 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A CD31A, NTER, PEML by analogy for ARG +ND3A2 CD31C CD32B CD32A 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32B CD32A, NTER, PEML by analogy for GLU +ND3A2 CD31C CD32B CD32C 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32B CD32C, NTER, alex by analogy for GLUP +ND3A2 CD31C CD32A CD2O2A 0.200 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A CD2O2A, NTER - ASP, jing +ND3A2 CD31C CD32C CD2O1A 1.432 1 0.00 ! NNEU, based on ND3P3A CD31C CD32C CD2O1A, PEML by analogy ASN NTER +ND3A2 CD31C CD32C CD2O1A 1.356 2 180.00 ! NNEU, based on ND3P3A CD31C CD32C CD2O1A, PEML by analogy ASN NTER +ND3A2 CD31C CD32C CD2O1A 0.038 3 180.00 ! NNEU, based on ND3P3A CD31C CD32C CD2O1A, PEML by analogy ASN NTER +ND3A2 CD31C CD32A SD31B 0.562 1 180.00 ! NNEU, based on ND3P3A CD31C CD32A SD31B, PEML by analogy CYS NTER +ND3A2 CD31C CD32A SD31B 0.192 2 180.00 ! NNEU, based on ND3P3A CD31C CD32A SD31B, PEML by analogy CYS NTER +ND3A2 CD31C CD32A SD31B 1.696 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A SD31B, PEML by analogy CYS NTER +ND3A2 CD31C CD32A OD31A 0.500 2 0.00 ! NNEU, based on ND3P3A CD31C CD32A OD31A, NTER, PEML by analogy for SER +ND3A2 CD31C CD32A OD31A 0.500 3 0.00 ! NNEU, based on ND3P3A CD31C CD32A OD31A, NTER, PEML by analogy for SER +ND3A2 CD31C CD31A OD31A 0.500 2 0.00 ! NNEU, based on ND3P3A CD31C CD31A OD31A, NTER, PEML by analogy for THR +ND3A2 CD31C CD31A OD31A 0.500 3 0.00 ! NNEU, based on ND3P3A CD31C CD31A OD31A, NTER, PEML by analogy for THR +CD33C ND2A3 CD2O1A OD2C1A 2.000 2 180.00 ! DMA, N,N-dimethylacetamide +CD33C ND2A3 CD2O1A CD33C 1.700 1 0.00 ! DMA, N,N-dimethylacetamide +CD33C ND2A3 CD2O1A CD33C 2.000 2 180.00 ! DMA, N,N-dimethylacetamide +CD2O1A ND2A3 CD33C HDA3A 0.000 3 0.00 ! DMA, N,N-dimethylacetamide +CD33C ND2A3 CD33C HDA3A 0.300 3 0.00 ! DMA, N,N-dimethylacetamide +CD32A ND2P1A CD2N1A ND2P1A 0.170 1 180.00 ! ARG, chi5 QM PES fit (PEML) +CD32A ND2P1A CD2N1A ND2P1A 2.210 2 180.00 ! ARG, chi5 QM PES fit (PEML) +CD32A ND2P1A CD2N1A ND2P1A 0.150 5 180.00 ! ARG, chi5 QM PES fit (PEML) +CD33A ND2P1A CD2N1A ND2P1A 0.170 1 180.00 ! ARG, chi5 QM PES fit (PEML) +CD33A ND2P1A CD2N1A ND2P1A 2.210 2 180.00 ! ARG, chi5 QM PES fit (PEML) +CD33A ND2P1A CD2N1A ND2P1A 0.150 5 180.00 ! ARG, chi5 QM PES fit (PEML) +HDP1B ND2P1A CD2N1A ND2P1A 1.900 2 180.00 ! ARG, c22 In c22 it is the same as [CD33A ND2P1A CD2N1] +CD32A CD32A ND2P1A CD2N1A 0.158 1 0.00 ! RMSE = 0.0117507, mguan24, fylin +CD32A CD32A ND2P1A CD2N1A 0.370 2 180.00 ! RMSE = 0.0117507, fylin +CD32A CD32A ND2P1A CD2N1A 0.048 3 180.00 ! RMSE = 0.0117507, fylin +CD2N1A ND2P1A CD32A HDA2A 0.000 3 0.00 ! ARG, c22 +HDP1B ND2P1A CD32A CD32A 0.000 3 0.00 ! ARG, c22 +HDP1B ND2P1A CD32A HDA2A 0.000 3 0.00 ! ARG, c22 +CD2N1A ND2P1A CD33A HDA3A 0.000 3 0.00 ! ARG, c22 +HDP1B ND2P1A CD33A HDA3A 0.000 3 0.00 ! ARG, c22 +CD2R5A ND2R5A CD2R5A CD2R5C 14.400 2 180.00 ! PYRR, pyrrole +CD2R5A ND2R5A CD2R5A HDR5A 2.600 2 180.00 ! PYRR, pyrrole +CD2R5B ND2R5A CD2R5A CD2R5A 14.000 2 180.00 ! IMID, imidazole +CD2R5B ND2R5A CD2R5A CD32A 3.000 2 180.00 ! HSD/4MIM, 4-methyl-imidazole +CD2R5B ND2R5A CD2R5A CD33A 3.000 2 180.00 ! 4MIM, 4-methyl-imidazole +CD2R5B ND2R5A CD2R5A HDR5A 3.000 2 180.00 ! IMID, imidazole +CD2R6D ND2R5A CD2R5A CD2R5C 9.520 2 180.00 ! INDO, indole +CD2R6D ND2R5A CD2R5A HDR5A 0.810 2 180.00 ! INDO, indole +HDP1A ND2R5A CD2R5A CD2R5A 1.100 2 180.00 ! IMID, imidazole +HDP1A ND2R5A CD2R5A CD2R5C 1.300 2 180.00 ! PYRR, pyrrole +HDP1A ND2R5A CD2R5A CD32A 1.000 2 180.00 ! HSD/4MIM, 4-methyl-imidazole +HDP1A ND2R5A CD2R5A CD33A 1.000 2 180.00 ! 4MIM, 4-methyl-imidazole +HDP1A ND2R5A CD2R5A HDR5A 0.000 2 180.00 ! IMID, imidazole +CD2R5A ND2R5A CD2R5B ND2R5B 14.000 2 180.00 ! IMID, imidazole +CD2R5A ND2R5A CD2R5B HDR5B 3.000 2 180.00 ! IMID, imidazole +CD2R6F ND2R5A CD2R5B ND2R5B 12.000 2 180.00 ! PUR0/1, purine, imidazole ring +CD2R6F ND2R5A CD2R5B HDR5B 4.700 2 180.00 ! PUR0/1, purine, imidazole ring +HDP1A ND2R5A CD2R5B ND2R5B 1.100 2 180.00 ! IMID, imidazole +HDP1A ND2R5A CD2R5B HDR5B 0.900 2 180.00 ! IMID, imidazole +CD2R5A ND2R5A CD2R6D CD2R6A 2.040 2 180.00 ! INDO, indole +CD2R5A ND2R5A CD2R6D CD2R6D 8.260 2 180.00 ! INDO, indole +HDP1A ND2R5A CD2R6D CD2R6A 0.250 2 180.00 ! INDO, indole +HDP1A ND2R5A CD2R6D CD2R6D 0.250 2 180.00 ! INDO, indole +CD2R5B ND2R5A CD2R6F ND2R6B 7.600 2 180.00 ! PUR1, purine, butterfly mode +CD2R5B ND2R5A CD2R6F CD2R6B 2.000 2 180.00 ! PUR1, purine, tautomer A, imidazole ring +CD2R5B ND2R5A CD2R6F CD2R6F 6.200 2 180.00 ! PUR0/1, purine, imidazole ring +HDP1A ND2R5A CD2R6F ND2R6B 1.000 2 180.00 ! PUR0, purine, tautomer B, imidazole ring +HDP1A ND2R5A CD2R6F CD2R6B 1.000 2 180.00 ! PUR1, purine, tautomer A, imidazole ring +HDP1A ND2R5A CD2R6F CD2R6F 2.700 2 180.00 ! PUR0/1, purine +CD2R5B ND2R5B CD2R5A CD2R5A 14.000 2 180.00 ! IMID, imidazole +CD2R5B ND2R5B CD2R5A CD32A 3.000 2 180.00 ! HSE, c22 +CD2R5B ND2R5B CD2R5A CD33A 3.000 2 180.00 ! HSE, c22, 4MIE +CD2R5B ND2R5B CD2R5A HDR5A 3.000 2 180.00 ! IMID, imidazole +CD2R5A ND2R5B CD2R5B ND2R5A 14.000 2 180.00 ! IMID, imidazole +CD2R5A ND2R5B CD2R5B HDR5B 3.000 2 180.00 ! IMID, imidazole +CD2R6F ND2R5B CD2R5B ND2R5A 11.500 2 180.00 ! PUR0/1, purine, imidazole ring +CD2R6F ND2R5B CD2R5F ND2R5A 11.500 2 180.00 ! jal +CD2R6F ND2R5B CD2R5B HDR5B 4.700 2 180.00 ! PUR0/1, purine, imidazole ring +CD2R6F ND2R5B CD2R5F HDR5B 4.700 2 180.00 ! jal +CD2R6F ND2R5E CD2R5F ND2R5D 14.000 2 180.00 ! ADE, jal +CD2R6F ND2R5E CD2R5F HDR5B 4.700 2 180.00 ! ADE, jal 06/15 +CD2R5B ND2R5B CD2R6F ND2R6B 7.600 2 180.00 ! PUR0, purine, butterfly mode +CD2R5F ND2R5B CD2R6F ND2R6B 7.600 2 180.00 ! jal +CD2R5B ND2R5B CD2R6F CD2R6B 2.000 2 180.00 ! PUR0, purine, tautomer B, imidazole ring +CD2R5F ND2R5B CD2R6F CD2R6B 2.000 2 180.00 ! jal +CD2R5B ND2R5B CD2R6F CD2R6F 6.700 2 180.00 ! PUR1, purine, butterfly mode +CD2R5F ND2R5B CD2R6F CD2R6F 6.700 2 180.00 ! ADE, jal +CD2R5F ND2R5E CD2R6F CD2O4A 2.000 2 180.00 ! GUA, jal +CD2R5F ND2R5E CD2R6F CD2R6C 2.000 2 180.00 ! ADE, jal +CD2R5F ND2R5E CD2R6F CD2R6F 6.700 2 180.00 ! ADE, jal +CD2R5E ND2R5C CD2R5D CD2R5D 14.000 2 180.00 ! IMIM, from IMID (EH) +CD2R5E ND2R5C CD2R5D CD32A 2.500 2 180.00 ! HSP, c22 +CD2R5E ND2R5C CD2R5D HDR5D 3.000 2 180.00 ! IMIM, from IMID (EH) +HDP1A ND2R5C CD2R5D CD2R5D 1.100 2 180.00 ! IMIM, from IMID (EH) +HDP1A ND2R5C CD2R5D CD32A 3.000 2 180.00 ! HSP, c22 +HDP1A ND2R5C CD2R5D HDR5D 0.000 2 180.00 ! IMIM, from IMID (EH) +CD2R5D ND2R5C CD2R5E ND2R5C 14.000 2 180.00 ! IMIM, from IMID (EH) +CD2R5D ND2R5C CD2R5E HDR5E 3.000 2 180.00 ! IMIM, from IMID (EH) +HDP1A ND2R5C CD2R5E ND2R5C 1.100 2 180.00 ! IMIM, from IMID (EH) +HDP1A ND2R5C CD2R5E HDR5E 0.900 2 180.00 ! IMIM, from IMID (EH) +CD2R6F ND2R5D CD2R5F ND2R5E 6.000 2 180.00 ! ADE, jal +CD2R6F ND2R5D CD2R5F HDR5B 3.500 2 180.00 ! ADE, va H8, jal +CD33A ND2R5D CD2R5F ND2R5E 1.000 2 180.00 ! ADE, jal +CD33A ND2R5D CD2R5F HDR5B 1.000 2 180.00 ! ADE, jal +HDP1A ND2R5D CD2R5F ND2R5B 1.000 2 180.00 ! IMID, jal +HDP1A ND2R5D CD2R5F ND2R5E 1.000 2 180.00 ! ADE, jal +HDP1A ND2R5D CD2R5F HDR5B 1.000 2 180.00 ! ADE, IMID, jal +CD2R5F ND2R5D CD2R6F ND2R6B 2.000 2 180.00 ! ADE, jal +CD2R5F ND2R5D CD2R6F CD2R6F 6.000 2 180.00 ! ADE, jal +CD33A ND2R5D CD2R6F ND2R6B 1.000 2 180.00 ! ADE, cmb +CD33A ND2R5D CD2R6F CD2R6F 1.000 2 180.00 ! ADE, cmb +HDP1A ND2R5D CD2R6F ND2R6B 1.500 2 180.00 ! ADE, cmb 04/10 +HDP1A ND2R5D CD2R6F CD2R6F 1.200 2 180.00 ! ADE, cmb 04/10 +CD2R5F ND2R5D CD33A HDA3A 0.000 3 0.00 ! ADE, jal +CD2R6F ND2R5D CD33A HDA3A 0.000 3 0.00 ! ADE, cmb +CD2R6B ND2R6A CD2R6B CD2R6A 2.200 2 180.00 ! PYR, pyridine +CD2R6B ND2R6A CD2R6B HDR6B 4.300 2 180.00 ! PYR, pyridine +CD2R6B ND2R6B CD2O4A ND2R6B 0.600 2 180.00 ! CYT, jal +CD2R6B ND2R6B CD2O4A ND2R6C 0.600 2 180.00 ! CYT, jal +CD2R6B ND2R6B CD2O4A OD2C1B 1.600 2 180.00 ! CYT, jal +CD2R6H ND2R6B CD2O4A ND2R6B 0.600 2 180.00 ! CYT, jal +CD2R6H ND2R6C CD2O4A ND2R6B 0.600 2 180.00 ! CYT, jal +CD2R6H ND2R6B CD2O4A ND2R6C 1.500 2 180.00 ! THY, jal +CD2R6H ND2R6C CD2O4A ND2R6C 1.500 2 180.00 ! THY, jal +CD2R6H ND2R6C CD2O4A OD2C1B 1.600 2 180.00 ! CYT, jal +CD33A ND2R6C CD2O4A ND2R6B 0.900 2 180.00 ! CYT, jal +CD33A ND2R6C CD2O4A ND2R6C 0.700 2 180.00 ! THY, jal +CD33A ND2R6C CD2O4A OD2C1B 0.900 2 180.00 ! CYT, jal +HDP1A ND2R6B CD2O4A ND2R6B 3.000 2 180.00 ! CYT, jal +HDP1A ND2R6B CD2O4A ND2R6C 1.600 2 180.00 ! THY, jal +HDP1A ND2R6B CD2O4A OD2C1B 3.000 2 180.00 ! CYT, jal +CD2O4A ND2R6B CD2R6B ND2B1 2.000 2 180.00 ! CYT, jal +CD2O4A ND2R6B CD2R6B CD2R6A 0.600 2 180.00 ! CYT, jal +CD2O4A ND2R6B CD2R6B CD2R6J 0.600 2 180.00 ! CYT, jal +CD2R6C ND2R6B CD2R6B CD2R6A 2.000 2 180.00 ! PYRM, pyrimidine +CD2R6C ND2R6B CD2R6B CD2R6F 7.800 2 180.00 ! PUR0/1, purine +CD2R6C ND2R6B CD2R6B CD2R6J 2.000 2 180.00 ! PYRM, pyrimidine, jal +CD2R6C ND2R6B CD2R6B HDR6B 10.740 2 180.00 ! PYRM, pyrimidine +CD2R6B ND2R6B CD2R6C ND2R6B 4.520 2 180.00 ! PYRM, pyrimidine +CD2R6B ND2R6B CD2R6C HDR6C 8.150 2 180.00 ! PYRM, pyrimidine +CD2R6C ND2R6B CD2R6C ND2B1 4.000 2 180.00 ! ADE, N6, cmb 04/10 +CD2R6C ND2R6B CD2R6C ND2R6B 1.800 2 180.00 ! ADE +CD2R6C ND2R6B CD2R6C CD2R6F 10.000 2 180.00 ! ADE, cmb 04/10 +CD2R6C ND2R6B CD2R6C HDR6C 6.500 2 180.00 ! ADE, va H2, jal +CD2R6F ND2R6B CD2R6C ND2R6B 0.100 2 180.00 ! PUR0/1, purine +CD2R6F ND2R6B CD2R6C HDR6C 6.500 2 180.00 ! PUR0/1, purine +CD2R6F ND2R6B CD2R6C ND2B1 4.000 2 180.00 ! GUA, cmb 04/10 +CD2R6F ND2R6B CD2R6C ND2R6C 2.000 2 180.00 ! GUA, cmb 04/10 +CD2R6C ND2R6B CD2R6F ND2R5A 7.600 2 180.00 ! PUR1, purine, butterfly mode +CD2R6C ND2R6B CD2R6F ND2R5B 7.600 2 180.00 ! PUR0, purine, butterfly mode +CD2R6C ND2R6B CD2R6F CD2R6F 7.800 2 180.00 ! PUR0/1, purine +CD2R6C ND2R6B CD2R6F ND2R5D 2.500 2 180.00 ! ADE, butterfly motion, jal +CD2O4A ND2R6C CD2R6H CD2R6J 0.600 2 180.00 ! CYT, jal +CD2O4A ND2R6C CD2R6H HDR6B 3.600 2 180.00 ! CYT, jal +CD33A ND2R6C CD2R6H CD2R6J 1.000 2 180.00 ! CYT, jal +CD33A ND2R6C CD2R6H HDR6B 1.000 2 180.00 ! CYT, cmb 04/10 +HDP1A ND2R6C CD2R6H CD2R6J 1.600 2 180.00 ! CYT, jal +HDP1A ND2R6C CD2R6H HDR6B 1.500 2 180.00 ! CYT, cmb 04/10 +CD2O4A ND2R6C CD33A HDA3A 0.000 3 0.00 ! CYT, jal +CD2R6H ND2R6C CD33A HDA3A 0.000 3 0.00 ! CYT, jal +CD2O4A ND2R6C CD2O4A ND2R6B 1.500 2 180.00 ! THY, jal +CD2O4A ND2R6C CD2O4A ND2R6C 1.500 2 180.00 ! THY, jal +CD2O4A ND2R6C CD2O4A OD2C1B 0.900 2 180.00 ! THY, jal +CD2O4A ND2R6C CD2O4A CD2R6J 0.900 2 180.00 ! THY, jal +CD2R6C ND2R6C CD2O4A OD2C1B 8.000 2 180.00 ! GUA, jal +CD2R6C ND2R6C CD2O4A CD2R6F 0.200 2 180.00 ! GUA, jal +HDP1A ND2R6C CD2O4A ND2R6B 3.800 2 180.00 ! THY, jal +HDP1A ND2R6C CD2O4A ND2R6C 3.800 2 180.00 ! THY, jal +HDP1A ND2R6C CD2O4A OD2C1B 0.000 2 180.00 ! THY, jal +HDP1A ND2R6C CD2O4A CD2R6F 3.600 2 180.00 ! GUA, jal +HDP1A ND2R6C CD2O4A CD2R6J 4.800 2 180.00 ! THY, jal +CD2O4A ND2R6C CD2R6C ND2B1 4.000 2 180.00 ! GUA, jal +CD2O4A ND2R6C CD2R6C ND2R6B 0.200 2 180.00 ! GUA, jal +HDP1A ND2R6C CD2R6C ND2B1 0.000 2 180.00 ! GUA, cmb 04/10 +HDP1A ND2R6C CD2R6C ND2R6B 3.600 2 180.00 ! GUA, cmb 04/10 +CD31C ND3A3 CD2O1A OD2C1A 2.500 2 180.00 ! PRO +CD31C ND3A3 CD2O1A CD31C 2.500 2 180.00 ! PRO +CD31C ND3A3 CD2O1A CD32C 2.500 2 180.00 ! PRO +CD31C ND3A3 CD2O1A CD32A 2.500 2 180.00 ! PRO +CD31C ND3A3 CD2O1A CD33C 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A OD2C1A 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A CD31C 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A CD32A 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A CD32C 2.500 2 180.00 ! PRO +CD32A ND3A3 CD2O1A CD33C 2.500 2 180.00 ! PRO +CD2O1A ND3A3 CD31C CD2O1A 0.300 1 0.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD2O1A 0.200 2 0.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD2O1A 2.600 3 0.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD2O2A 0.200 3 0.00 ! PRO, CTER +CD2O1A ND3A3 CD31C CD32A 0.300 1 180.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD32A 0.700 2 180.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C CD32A 0.700 3 0.00 ! PRO FIT PES PEML CHI5 +CD2O1A ND3A3 CD31C HDA1A 0.200 3 0.00 ! PRO +CD32A ND3A3 CD31C CD2O1A 1.800 1 0.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD2O1A 1.200 2 0.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD2O1A 0.500 3 180.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD2O2A 0.200 3 0.00 ! PRO, CTER +CD32A ND3A3 CD31C CD32A 0.500 1 180.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD32A 1.700 2 180.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C CD32A 1.600 3 0.00 ! PRO FIT PES PEML CHI5 +CD32A ND3A3 CD31C HDA1A 0.200 3 0.00 ! PRO +CD2O1A ND3A3 CD32A CD32A 2.400 1 180.00 ! PRO FIT PES PEML CHI4 +CD2O1A ND3A3 CD32A CD32A 1.000 2 0.00 ! PRO FIT PES PEML CHI4 +CD2O1A ND3A3 CD32A CD32A 0.700 3 180.00 ! PRO FIT PES PEML CHI4 +CD2O1A ND3A3 CD32A HDA2A 0.200 3 0.00 ! PRO FIXED PES PEML CHI4 +CD31C ND3A3 CD32A CD32A 0.600 1 180.00 ! PRO FIT PES PEML CHI4 +CD31C ND3A3 CD32A CD32A 0.900 2 180.00 ! PRO FIT PES PEML CHI4 +CD31C ND3A3 CD32A CD32A 1.000 3 0.00 ! PRO FIT PES PEML CHI4 +CD31C ND3A3 CD32A HDA2A 0.200 3 0.00 ! PRO FIXED PES PEML CHI4 +CD32C ND3A3 CD32C CD32A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +ND3A3 CD32C CD32A CD32A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +HDP1A ND3A3 CD31C CD32A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +CD32C CD32A CD32A CD32C 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +CD32C ND3A3 CD32C HDA2A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +ND3A3 CD32C CD32A HDA2A 0.200 3 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +HDP1A ND3A3 CD32C CD32A 0.000 1 0.00 ! PRLD, pyrrolidine, PEML % CHECK THESE ? +CD32A ND3P2A CD31C CD32A 0.260 3 0.00 ! N-terminal PRO +CD32A ND3P2A CD31C HDA1C 0.200 3 0.00 ! N-terminal PRO +CD32A ND3P2A CD31C CD2O1A 0.260 3 0.00 ! N-terminal PRO +CD33A ND3P2A CD32A CD33A 0.260 3 0.00 ! NC5/CHOL, qm, EH 2007, ammonium cation +HDA2C CD32A ND3P2A CD31C 0.260 3 0.00 ! N-terminal PRO +CD31C ND3P2A CD32A CD32A 0.260 3 0.00 ! N-terminal PRO +HDA1C CD31C CD32A HDA2A 0.200 3 0.00 ! N-terminal PRO +HDA1C CD31C CD31A CD32A 0.200 3 0.00 ! PEML by analogy ILE +HDA1C CD31C CD32A CD31A 0.200 3 0.00 ! PEML by analogy LEU +HDA1C CD31C CD32A CD32A 0.200 3 0.00 ! N-terminal PRO +HDA1C CD31C CD32B CD32A 0.200 3 0.00 ! PEML by analogy GLU +HDA1C CD31C CD32B CD32C 0.200 3 0.00 ! alex by analogy GLUP +CD33A ND3P2A CD32A HDA2C 0.260 3 0.00 ! NC4, charmm27, ammonium cation +CD32A ND3P2A CD33A HDA3C 0.230 3 0.00 ! NC4, charmm27 , ammonium cation +CD33A ND3P2A CD33A HDA3C 0.230 3 0.00 ! NC4, charmm27, ammonium cation +HDP1B ND3P2A CD31A CD2O1A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 +HDP1B ND3P2A CD31C CD2O1A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 +HDP1B ND3P2A CD31A CD2O2A 0.320 3 0.00 ! NTER, zwitterionic dipeptide %% +HDP1B ND3P2A CD31A CD2O3A 0.320 3 0.00 ! CNEU/NTER, CNEU %% +HDP1B ND3P2A CD31C CD2O3A 0.320 3 0.00 ! CNEU/NTER, CNEU %% +HDP1B ND3P2A CD31A CD31A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P2A CD31A CD32A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P2A CD31C CD32A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P2A CD31A CD33A 0.320 3 0.00 ! CNEU/NTER, NTER-CT3 ETAM, qm, EH 2007 %% +HDP1B ND3P2A CD31A HDA1C 0.100 3 0.00 ! CNEU/NTER, ETAM, qm, EH 2007 %% +HDP1B ND3P2A CD31C HDA1C 0.100 3 0.00 ! CNEU/NTER, ETAM, qm, EH 2007 %% +HDP1B ND3P2A CD32A CD2O1A 0.320 3 0.00 ! NTER, ETAM, gly +HDP1B ND3P2A CD32C CD2O1A 0.320 3 0.00 ! NTER, ETAM, gly +HDP1B ND3P2A CD32A CD32A 0.320 3 0.00 ! ETAM, qm, EH 2007, ammonium cation, for lipids +HDP1B ND3P2A CD32A CD33A 0.320 3 0.00 ! ETAM, qm, EH 2007, ammonium cation +HDP1B ND3P2A CD32A HDA2C 0.100 3 0.00 ! ETAM, charmm27, gly +HDP1B ND3P2A CD32C HDA2C 0.100 3 0.00 ! ETAM, charmm27, gly +HDP1B ND3P2A CD33A HDA3C 0.100 3 0.00 ! NC1, charmm27 (etam), not necessary for lipid, NH4+ +HDP1B ND3P3A CD31A CD2O1A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 +HDP1B ND3P3A CD31C CD2O1A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 +HDP1B ND3P3A CD31A CD2O2A 0.320 3 0.00 ! NTER, zwitterionic dipeptide %% +HDP1B ND3P3A CD31C CD2O2A 0.320 3 0.00 ! NTER, zwitterionic dipeptide %% +HDP1B ND3P3A CD32C CD2O2A 0.320 3 0.00 ! NTER, zwitterionic dipeptide %% +HDP1B ND3P3A CD31A CD2O3A 0.320 3 0.00 ! CNEU/NTER, CNEU %% +HDP1B ND3P3A CD31C CD2O3A 0.320 3 0.00 ! CNEU/NTER, CNEU %% +HDP1B ND3P3A CD31A CD31A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P3A CD31C CD31A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P3A CD31A CD32A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P3A CD31C CD32A 0.320 3 0.00 ! NTER, ETAM, qm, EH 2007 *DELETE* +HDP1B ND3P3A CD31C CD32B 0.320 3 0.00 ! PEML by analogy, GLU, NTER +HDP1B ND3P3A CD31C CD32C 0.320 3 0.00 ! PEML by analogy, ASN, NTER +HDP1B ND3P3A CD31A CD33A 0.320 3 0.00 ! CNEU/NTER, NTER-CT3 ETAM, qm, EH 2007 %% +HDP1B ND3P3A CD31C CD33A 0.320 3 0.00 ! CNEU/NTER, NTER-CT3 ETAM, qm, EH 2007 %% +HDP1B ND3P3A CD31A HDA1C 0.100 3 0.00 ! CNEU/NTER, ETAM, qm, EH 2007 %% +HDP1B ND3P3A CD31C HDA1C 0.100 3 0.00 ! CNEU/NTER, ETAM, qm, EH 2007 %% +HDP1B ND3P3A CD32A CD2O1A 0.320 3 0.00 ! NTER, ETAM, gly +HDP1B ND3P3A CD32C CD2O1A 0.320 3 0.00 ! NTER, ETAM, gly +HDP1B ND3P3A CD32A CD32A 0.305 1 180.00 ! NC5, LYS, lipids, PE headgroup, reevaluate +HDP1B ND3P3A CD32A CD32A 0.276 3 0.00 ! NC5, LYS +HDP1B ND3P3A CD32A CD32A 0.934 4 180.00 ! NC5, LYS +HDP1B ND3P3A CD32A CD32A 1.670 5 0.00 ! NC5, LYS +HDP1B ND3P3A CD32A CD32A 0.047 6 0.00 ! NC5, LYS +HDP1B ND3P3A CD32A CD33A 0.320 3 0.00 ! ETAM, qm, EH 2007, ammonium cation +HDP1B ND3P3A CD32A HDA2C 0.100 3 0.00 ! ETAM, charmm27, ammonium cation +HDP1B ND3P3A CD32C HDA2C 0.100 3 0.00 ! ETAM, charmm27, gly +HDP1B ND3P3A CD33A HDA3C 0.100 3 0.00 ! NC1, charmm27 (etam), not necessary for lipid, ammonium cation +HDP1B ND3P3A CD32A HDA2A 0.100 3 0.00 ! NC1, lipid +CD325B OD305A CD315B CD325B 0.500 3 0.00 ! TF2M, cmb +CD325B OD305A CD315B CD33A 0.300 3 0.00 ! TF2M, cmb +CD325B OD305A CD315B HDA1R5 0.300 3 0.00 ! TF2M, cmb +CD315B OD305A CD325B CD325B 0.500 3 0.00 ! TF2M, cmb +CD315B OD305A CD325B HDA2R5 0.300 3 0.00 ! TF2M, cmb +CD325B OD305A CD325B CD325B 0.500 3 0.00 ! THF, viv +CD325B OD305A CD325B HDA2R5 0.300 3 0.00 ! THF, viv +CD326B OD306A CD326B CD326B 0.52702 1 180.00 ! THP, sng 1/06 +CD326B OD306A CD326B CD326B 0.68297 2 0.00 ! THP, sng 1/06 +CD326B OD306A CD326B CD326B 0.20977 3 180.00 ! THP, sng 1/06 +CD326B OD306A CD326B CD326B 0.15037 4 0.00 ! THP, sng 1/06 +CD326B OD306A CD326B HDA2E 0.284 3 0.00 ! DMEE, viv +CD32A OD30A CD32A CD32A 0.570 1 0.00 ! DMOE, ATM +CD32A OD30A CD32A CD32A 0.290 2 0.00 ! DMOE, ATM +CD32A OD30A CD32A CD32A 0.430 3 0.00 ! DMOE, ATM +CD32A OD30A CD32A CD33A 0.400 1 0.00 ! DEET, ATM +CD32A OD30A CD32A CD33A 0.490 3 0.00 ! DEET +CD32A OD30A CD32A HDA2A 0.284 3 0.00 ! DEET, alex +CD33A OD30A CD32A CD32A 0.570 1 0.00 ! DMOE, 1,2-dimethoxyethane (DMOE), 2/12/05, ATM +CD33A OD30A CD32A CD32A 0.290 2 0.00 ! DMOE, ATM +CD33A OD30A CD32A CD32A 0.430 3 0.00 ! DMOE, ATM +CD33A OD30A CD32A CD33A 0.400 1 0.00 ! MEE, viv +CD33A OD30A CD32A CD33A 0.490 3 0.00 ! MEE, viv +CD33A OD30A CD32A HDA2A 0.284 3 0.00 ! DEET, alex +CD32E OD30A CD32E CD32A 0.570 1 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32A 0.290 2 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32A 0.430 3 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32E 0.570 1 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32E 0.290 2 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD32E 0.430 3 0.00 ! DMOE, ATM +CD32E OD30A CD32E CD33A 0.400 1 0.00 ! DEET, ATM +CD32E OD30A CD32E CD33A 0.490 3 0.00 ! DEET +CD32E OD30A CD32E HDA2E 0.284 3 0.00 ! DEET, alex +CD33E OD30A CD32E CD32A 0.570 1 0.00 ! DMOE, +CD33E OD30A CD32E CD32A 0.290 2 0.00 ! DMOE, ATM +CD33E OD30A CD32E CD32A 0.430 3 0.00 ! DMOE, ATM +CD33E OD30A CD32E CD32E 0.570 1 0.00 ! DMOE, +CD33E OD30A CD32E CD32E 0.290 2 0.00 ! DMOE, ATM +CD33E OD30A CD32E CD32E 0.430 3 0.00 ! DMOE, ATM +CD33E OD30A CD32E CD33A 0.400 1 0.00 ! MEE, viv +CD33E OD30A CD32E CD33A 0.490 3 0.00 ! MEE, viv +CD33E OD30A CD32E HDA2E 0.284 3 0.00 ! DEET, alex +CD32A OD30A CD33A HDA3A 0.284 3 0.00 ! DEET, alex +CD33A OD30A CD33A HDA3A 0.284 3 0.00 ! DME, viv +CD32E OD30A CD33E HDA3A 0.284 3 0.00 ! DEET, alex +CD33E OD30A CD33E HDA3A 0.284 3 0.00 ! DME, viv +HDA1A CD31C CD32C HDA2A 0.200 3 0.00 ! Lipid, alkane +CD33A CD31C CD32C HDA2A 0.200 3 0.00 ! GLYC, alkane, lipid +CD32A CD31C CD32C HDA2A 0.200 3 0.00 ! GLYC, alkane, lipid +CD32B CD31C CD32C HDA2A 0.200 3 0.00 ! GLYC, alkane, lipid +CD32C CD31C CD32A HDA2A 0.190 3 0.00 ! GLYC, alkane +CD32C CD31C CD32B HDA2A 0.190 3 0.00 ! GLYC, alkane +CD32C CD31C CD33A HDA3A 0.190 3 0.00 ! GLYC, alkane, lipid +CD32C CD32A CD32A HDA2A 0.160 3 0.00 ! Lipid-H, alkane, ester +!lipid_opt_2020: glycerol linker parameters updated. Lipid specific parameters for global +!optimization moved to lipid toppar stream file. These are commented out below. +!EAS: C-OM-C2-C3, beta1 +CD2O3A OD30C CD32C CD33A 1.759 1 180.00 ! EAS, C-OM-C2-C3, 2020, model cmpd only +CD2O3A OD30C CD32C CD33A 0.126 2 180.00 ! EAS +CD2O3A OD30C CD32C CD33A 0.148 3 0.00 ! EAS +CD2O3A OD30C CD32C CD32A 1.759 1 180.00 ! EAS, C-OM-C2-C3, 2020, model cmpd only +CD2O3A OD30C CD32C CD32A 0.126 2 180.00 ! EAS +CD2O3A OD30C CD32C CD32A 0.148 3 0.00 ! EAS +CD2O3A OD30C CD31C CD33A 1.759 1 180.00 ! EAS, C-OM-C2-C3, 2020, model cmpd only +CD2O3A OD30C CD31C CD33A 0.126 2 180.00 ! EAS +CD2O3A OD30C CD31C CD33A 0.148 3 0.00 ! EAS +CD33C OD30C CD2O3A CD31C 0.493 1 0.00 ! MAS, C2-OM-C-C1, 2020, model cmpd only +CD33C OD30C CD2O3A CD31C 3.457 2 180.00 ! MAS +CD33C OD30C CD2O3A CD31C 0.315 3 0.00 ! MAS +CD33C OD30C CD2O3A CD32C 2.114 1 180.00 ! EAS, C2-OM-C-C1, 2020, model cmpd only +CD33C OD30C CD2O3A CD32C 3.449 2 180.00 ! EAS +CD33C OD30C CD2O3A CD32C 0.643 3 0.00 ! EAS +CD33C OD30C CD2O3A CD33C 0.493 1 0.00 ! MAS, C2-OM-C-C1, 2020, model cmpd only +CD33C OD30C CD2O3A CD33C 3.457 2 180.00 ! MAS +CD33C OD30C CD2O3A CD33C 0.315 3 0.00 ! MAS +CD32C OD30C CD2O3A CD31C 2.114 1 180.00 ! EAS, C2-OM-C-C1, 2020, model cmpd only +CD32C OD30C CD2O3A CD31C 3.449 2 180.00 ! EAS +CD32C OD30C CD2O3A CD31C 0.643 3 0.00 ! EAS +CD32C OD30C CD2O3A CD33C 2.114 1 180.00 ! EAS, C2-OM-C-C1, 2020, model cmpd only +CD32C OD30C CD2O3A CD33C 3.449 2 180.00 ! EAS +CD32C OD30C CD2O3A CD33C 0.643 3 0.00 ! EAS +CD31C OD30C CD2O3A CD33C 2.114 1 180.00 ! EAS, C2-OM-C-C1, 2020, model cmpd only +CD31C OD30C CD2O3A CD33C 3.449 2 180.00 ! EAS +CD31C OD30C CD2O3A CD33C 0.643 3 0.00 ! EAS +CD33A CD31C CD32C OD30C 0.334 1 180.00 ! GLYC, theta3_prime, model compound +CD33A CD31C CD32C OD30C 0.556 2 180.00 ! GLYC +CD33A CD31C CD32C OD30C 2.905 3 0.00 ! GLYC +OD2C3A CD2O3A OD30C CD32C 2.500 2 180.00 ! MAS, O-C-OM-C2, model cmpd only +OD2C3A CD2O3A CD32C CD32A 0.000 3 0.00 ! MPRO, O-C-C1-C3, O22=C21-C22-C23, beta3_prime +OD2C3A CD2O3A CD32C CD33A 0.000 3 0.00 ! MPRO, O-C-C1-C3, model cmpd only +! +OD30C CD2O3A CD32C ND2A2 0.200 3 0.00 ! CT1, c22, gly +OD30C CD2O3A CD32C CD33A 0.230 1 0.00 ! MPRO, OM-C-C1-C3, model cmpd only +OD30C CD2O3A CD32C CD33A 0.372 2 180.00 ! MPRO +OD30C CD2O3A CD32C CD33A 0.066 3 180.00 ! MPRO +OD30C CD2O3A CD32C HDA2A 0.000 3 180.00 ! MAS, PEML 2009 +CD2O3A CD32C CD32A CD33A 0.168 1 180.00 ! MBUT, C-C1-C3-C4, 2020, model cmpd only +CD2O3A CD32C CD32A CD33A 0.018 2 0.00 ! MBUT +CD2O3A CD32C CD32A CD33A 0.453 3 180.00 ! MBUT +OD30C CD2O3A CD31C HDA1A 0.200 3 180.00 ! CT1, MAS +OD30C CD32C CD31C HDA1A 0.200 3 0.00 ! EAS +OD30C CD31C CD32C HDA2A 0.200 3 0.00 ! EAS +CD2O3A OD30C CD31C HDA1A 0.200 3 180.00 ! MAS +CD2O3A OD30C CD32C HDA2A 0.200 3 180.00 ! MAS, PEML 2009 +CD2O3A OD30C CD33C HDA3A 0.200 3 180.00 ! MAS, PEML 2009 +CD2O3A CD32C CD32A HDA2A 0.200 3 0.00 ! alkane, ester, lipid specific +CD2O3A CD32C CD33A HDA3A 0.200 3 0.00 ! alkane, ester, lipid specific +HDP1A OD31F CD2O3A OD2C3A 1.110 2 180.00 ! ACEH, PEML +HDP1A OD31F CD2O3A CD31A 3.800 2 180.00 ! CNEU/ACEH, PEML +HDP1A OD31F CD2O3A CD31C 3.800 2 180.00 ! CNEU/ACEH, PEML +HDP1A OD31F CD2O3A CD32C 3.800 2 180.00 ! FROM ACEH, PEML, gly +HDP1A OD31F CD2O3A CD33C 3.760 2 180.00 ! ACEH, PEML +HDP1A OD31A CD2R6A CD2R6A 0.990 2 180.00 ! PHEN, phenol +HDP1A OD31A CD31A CD32A 1.660 1 0.00 ! BUO2, 2-butanol +HDP1A OD31A CD31A CD32A 0.120 2 0.00 ! BUO2, 2-butanol +HDP1A OD31A CD31A CD32A 0.340 3 0.00 ! BUO2, 2-butanol +HDP1A OD31A CD315A CD325A 1.660 1 0.00 ! CPO1, from BUO2, 2-butanol, cmb needs test +HDP1A OD31A CD315A CD325A 0.120 2 0.00 ! CPO1, from BUO2, 2-butanol, cmb needs test +HDP1A OD31A CD315A CD325A 0.340 3 0.00 ! CPO1, from BUO2, 2-butanol, cmb needs test +HDP1A OD31A CD31A CD33A 1.660 1 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A CD33A 0.120 2 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A CD33A 0.340 3 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A HDA1A 0.060 1 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A HDA1A 0.060 2 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD31A HDA1A 0.000 3 0.00 ! PRO2, 2-propanol +HDP1A OD31A CD315A HDA1R5 0.060 1 0.00 ! CPO1, from PRO2, 2-propanol, needs test +HDP1A OD31A CD315A HDA1R5 0.060 2 0.00 ! CPO1, from PRO2, 2-propanol, needs test +HDP1A OD31A CD315A HDA1R5 0.000 3 0.00 ! CPO1, from PRO2, 2-propanol, needs test +HDP1A OD31A CD32A CD32A 1.250 1 0.00 ! ETAM, from ethanol +HDP1A OD31A CD32A CD32A 0.350 2 0.00 ! ETAM +HDP1A OD31A CD32A CD32A 0.360 3 0.00 ! ETAM +HDP1A OD31A CD32A CD33A 1.250 1 0.00 ! ETOH, ethanol +HDP1A OD31A CD32A CD33A 0.350 2 0.00 ! ETOH, ethanol +HDP1A OD31A CD32A CD33A 0.360 3 0.00 ! ETOH, ethanol +HDP1A OD31A CD32A HDA2A 0.140 2 0.00 ! ETOH, ethanol +HDP1A OD31A CD32A HDA2A 0.130 3 0.00 ! ETOH, ethanol +HDP1A OD31A CD33B HDA3B 0.179 3 0.00 ! MEOH, methanol +HDP1A OD31B CD32A CD32A 1.050 1 0.00 ! PRO1, 1-propanol +HDP1A OD31B CD32A CD32A 0.370 2 0.00 ! PRO1, 1-propanol +HDP1A OD31B CD32A CD32A 0.340 3 0.00 ! PRO1, 1-propanol +HDP1A OD31B CD32A HDA2A 0.140 2 0.00 ! PRO1, 1-propanol +HDP1A OD31B CD32A HDA2A 0.130 3 0.00 ! PRO1, 1-propanol +HDP1A OD31C CD2R6A CD2R6A 0.990 2 180.00 ! PHEN, phenol +CD33A SD30A CD32A CD32A 0.2577 1 0.00 ! MET/EMS, chi3, sig fig,! +CD33A SD30A CD32A CD32A 0.4111 2 0.00 ! MET/EMS, chi3 +CD33A SD30A CD32A CD32A 0.5999 3 0.00 ! MET/EMS, chi3 +CD33A SD30A CD32A CD33A 0.2577 1 0.00 ! EMS +CD33A SD30A CD32A CD33A 0.4111 2 0.00 ! EMS +CD33A SD30A CD32A CD33A 0.5999 3 0.00 ! EMS +CD33A SD30A CD32A HDA2A 0.2800 3 0.00 ! EMS +CD32A SD30A CD33A HDA3A 0.2800 3 0.00 ! EMS +CD33A SD30A CD33A HDA3A 0.2800 3 0.00 ! DMS +CD32A SD30B SD30B CD32A 0.8123 1 0.00 ! DISU/DMDS +CD32A SD30B SD30B CD32A 3.8234 2 0.00 ! DISU/DMDS +CD32A SD30B SD30B CD32A 1.0123 3 0.00 ! DISU/DMDS +CD33A SD30B SD30B CD33A 0.8123 1 0.00 ! DMDS +CD33A SD30B SD30B CD33A 3.8234 2 0.00 ! DMDS +CD33A SD30B SD30B CD33A 1.0123 3 0.00 ! DMDS +SD30B SD30B CD32A CD31C 0.200 3 0.00 ! DISU, chi2, c22 +SD30B SD30B CD32A HDA2A 0.2777 3 0.00 ! DISU/DMDS +SD30B SD30B CD33A HDA3A 0.2777 3 0.00 ! DMDs +HDP1A SD31A CD33A HDA3A 0.203 3 0.00 ! MESH +HDP1A SD31B CD32A CD32A 0.280 1 180.00 ! PRSH +HDP1A SD31B CD32A CD32A 0.255 2 0.00 ! PRSH +HDP1A SD31B CD32A CD32A 0.365 3 0.00 ! PRSH +HDP1A SD31B CD32A CD33A 0.240 1 180.00 ! ETSH +HDP1A SD31B CD32A CD33A 0.200 2 0.00 ! ETSH +HDP1A SD31B CD32A CD33A 0.420 3 0.00 ! ETSH +HDP1A SD31B CD32A HDA2A 0.140 2 0.00 ! ETSH +HDP1A SD31B CD32A HDA2A 0.130 3 0.00 ! ETSH +ND2R6C CD2O4A CD2R6J CD2R6H 1.800 2 180.00 ! THY, jal +ND2R6C CD2O4A CD2R6J CD33A 1.000 2 180.00 ! THY, jal +ND2R6C CD2O4A CD2R6J HDR6A 1.000 2 180.00 ! URA jal +OD2C1B CD2O4A CD2R6J CD2R6H 1.000 2 180.00 ! THY, jal +OD2C1B CD2O4A CD2R6J CD33A 1.000 2 180.00 ! THY, jal +OD2C1B CD2O4A CD2R6J HDR6A 6.000 2 180.00 ! URA, jal +ND2R6C CD2O4A CD2R6F ND2R5E 2.000 2 180.00 ! GUA, jal +ND2R6C CD2O4A CD2R6F CD2R6F 0.200 2 180.00 ! GUA, jal +OD2C1B CD2O4A CD2R6F ND2R5E 0.000 2 180.00 ! GUA, jal +OD2C1B CD2O4A CD2R6F CD2R6F 8.000 2 180.00 ! GUA, jal +ND2A1 CD2O1A CD31A ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A1 CD2O1A CD31A ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND2A1 CD2O1A CD31C ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A1 CD2O1A CD31C ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31A ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31A ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31C ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31C ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND3A3 CD2O1A CD31C ND3P3A 0.300 1 180.00 ! NTER-CT3 pseud-psi %% +ND2A3 CD2O1A CD31C ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +ND2A2 CD2O1A CD31A CD31A 0.000 3 0.00 ! NTER +ND2A2 CD2O1A CD31A CD32A 0.000 3 0.00 ! NTER +ND2A2 CD2O1A CD31A CD33A 0.000 3 0.00 ! NTER +ND2A2 CD2O1A CD31A HDA1C 0.000 3 180.00 ! NTER +ND2A2 CD2O1A CD31C HDA1C 0.000 3 180.00 ! N-terminal PRO +OD2C1A CD2O1A CD31A ND3P3A 0.300 1 0.00 ! NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31A ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31C ND3P3A 0.300 1 0.00 ! NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31C ND3P3A 2.400 2 180.00 ! NTER-CT3 pseud-psi %% +OD2C1A CD2O1A CD31A ND3P2A 0.000 3 0.00 ! NTER-CT3 PRO +OD2C1A CD2O1A CD31C ND3P2A 0.000 3 0.00 ! NTER-CT3 PRO +OD2C1A CD2O1A CD31A CD31A 0.000 1 0.00 ! NTER +OD2C1A CD2O1A CD31A CD32A 0.000 1 0.00 ! NTER +OD2C1A CD2O1A CD31A CD33A 0.000 1 0.00 ! NTER +OD2C1A CD2O1A CD31A HDA1C 0.000 3 180.00 ! NTER +OD2C1A CD2O1A CD31C HDA1C 0.000 3 180.00 ! NTER +ND2A1 CD2O1A CD31C ND2A2 0.000 1 0.00 ! CT2, guess +ND2A1 CD2O1A CD31C CD33A 0.000 1 0.00 ! CT2, guess +ND2A1 CD2O1A CD31C CD32C 0.000 1 0.00 ! PEML by analogy, ASN CT2 +ND2A1 CD2O1A CD31C HDA1A 0.200 3 0.00 ! CT2, alkanes +ND2A1 CD2O1A CD31C HDA1C 0.200 3 0.00 ! CT2, alkanes +ND2A2 CD2O1A CD31C ND2A2 0.000 3 180.00 ! ALAD, psi, cmap +ND2A2 CD2O1A CD31C ND3A3 0.200 3 0.00 ! PRO +ND2A2 CD2O1A CD31C CD31A 0.000 1 0.00 ! ILE/VAL, c22 +ND2A2 CD2O1A CD31C CD32A 0.000 1 0.00 ! GLN, c22 +ND2A2 CD2O1A CD31C CD32B 0.000 1 0.00 ! GLU, from ND2A2 CD2O1A CD31C CD32A +ND2A2 CD2O1A CD31C CD32C 0.000 1 0.00 ! ASN, c22 +ND2A2 CD2O1A CD31C CD33A 0.000 1 0.00 ! ALAD, will effect psi +ND2A2 CD2O1A CD31C HDA1A 0.200 3 0.00 ! ALAD +ND3A3 CD2O1A CD31C ND2A2 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD32C ND2A2 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C ND3A3 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C CD31A 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C CD32A 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C CD32C 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C CD33A 0.200 3 0.00 ! PRO, adjacent to NTER +ND3A3 CD2O1A CD31C HDA1A 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD31C HDA1C 0.200 3 0.00 ! PRO +OD2C1A CD2O1A CD31C ND2A2 0.000 1 0.00 ! ALAD, psi, cmap +OD2C1A CD2O1A CD31C ND3A3 0.200 3 0.00 ! PRO +OD2C1A CD2O1A CD31C CD31A 1.400 1 0.00 ! ILE/VAL, c22 +OD2C1A CD2O1A CD31C CD32A 1.400 1 0.00 ! GLN, c22 +OD2C1A CD2O1A CD31C CD32B 1.400 1 0.00 ! GLU, from OD2C1A CD2O1A CD31C CD32A +OD2C1A CD2O1A CD31C CD32C 1.400 1 0.00 ! ASN, c22 +OD2C1A CD2O1A CD31C CD33A 3.920 1 0.00 ! ALAD, will effect psi +OD2C1A CD2O1A CD31C HDA1A 0.230 3 0.00 ! ALAD +ND2A2 CD2O1A CD32A ND3P3A 0.000 1 0.00 ! NTER, gly +ND2A2 CD2O1A CD32C ND3P3A 0.000 1 0.00 ! NTER, gly +ND2A2 CD2O1A CD31C ND3P2A 0.000 1 0.00 ! NTER, gly +ND3A3 CD2O1A CD31C ND3P2A 0.000 1 0.00 ! NTER PRO followed by PRO +ND2A2 CD2O1A CD32A HDA2C 0.200 3 0.00 ! GLYD +ND2A2 CD2O1A CD32C HDA2C 0.200 3 0.00 ! GLYD +ND3A3 CD2O1A CD32A ND3P3A 0.200 3 0.00 ! PRO, adjacent to NTER +ND3A3 CD2O1A CD32C ND3P3A 0.200 3 0.00 ! PRO, adjacent to NTER +ND3A3 CD2O1A CD32A HDA2C 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD32C HDA2C 0.200 3 0.00 ! PRO +ND3A3 CD2O1A CD32C HDA2A 0.200 3 0.00 ! PRO +OD2C1A CD2O1A CD32A ND3P3A 0.000 1 0.00 ! NTER, gly +OD2C1A CD2O1A CD32C ND3P3A 0.000 1 0.00 ! NTER, gly +OD2C1A CD2O1A CD32A HDA2C 0.230 3 0.00 ! GLYD +OD2C1A CD2O1A CD32C HDA2C 0.230 3 0.00 ! GLYD +ND2A1 CD2O1A CD32C ND2A2 0.000 1 0.00 ! CT2, guess, gly +ND2A1 CD2O1A CD32C CD32A 0.000 1 0.00 ! GLN, c22, chi3 +ND2A1 CD2O1A CD32C HDA2A 0.000 1 0.00 ! ASN, c22 +ND2A2 CD2O1A CD32C ND2A2 0.000 3 180.00 ! GLYD, psi, cmap +ND2A2 CD2O1A CD32C HDA2A 0.200 3 0.00 ! GLYD +OD2C1A CD2O1A CD32C ND2A2 0.000 3 180.00 ! GLYD, psi, cmap +OD2C1A CD2O1A CD32C CD32A 1.400 1 0.00 ! GLN, c22, chi3 +OD2C1A CD2O1A CD32C HDA2A 0.230 3 0.00 ! GLYD +ND2A1 CD2O1A CD33C HDA3A 0.079 3 180.00 ! ACEM +ND2A2 CD2O1A CD33C HDA3A 0.200 3 0.00 ! NMA +ND2A3 CD2O1A CD33C HDA3A 0.000 3 180.00 ! DMA, N,N-dimethylacetamide +ND3A3 CD2O1A CD33C HDA3A 0.200 3 0.00 ! PRO +OD2C1A CD2O1A CD33C HDA3A 0.230 3 0.00 ! NMA +OD2C2A CD2O2A CD31A ND3P3A 0.900 2 180.00 ! NTER, zwitterionic dipeptide also NTER-CT3 %% +OD2C2A CD2O2A CD31C ND3P3A 0.900 2 180.00 ! NTER, zwitterionic dipeptide also NTER-CT3 %% +OD2C2A CD2O2A CD32C ND3P3A 0.900 2 180.00 ! NTER, zwitterionic dipeptide also NTER-CT3 %% +OD2C2A CD2O2A CD31A CD31A 0.000 1 0.00 ! CTER +OD2C2A CD2O2A CD31A CD32A 0.000 1 0.00 ! CTER +OD2C2A CD2O2A CD31A CD33A 0.000 1 0.00 ! NTER, +OD2C2A CD2O2A CD31A HDA1C 0.000 3 180.00 ! NTER +OD2C2A CD2O2A CD31C ND2A2 3.000 1 0.00 ! CTER, PEML, pseudo-psi from ACE-CTER % +OD2C2A CD2O2A CD31C ND2A2 2.000 2 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER % +OD2C2A CD2O2A CD31C ND3A3 0.200 3 0.00 ! PRO, CTER +OD2C2A CD2O2A CD31C CD31A 0.000 1 0.00 ! CTER, PEML, Val/Ile +OD2C2A CD2O2A CD31C CD31A 0.000 2 180.00 ! CTER, PEML, Val/Ile +OD2C2A CD2O2A CD31C CD32A 0.000 1 0.00 ! CTER, PEML, Leu +OD2C2A CD2O2A CD31C CD32A 0.000 2 180.00 ! CTER, PEML, Leu +OD2C2A CD2O2A CD31C CD32B 0.000 1 0.00 ! CTER, Glu +OD2C2A CD2O2A CD31C CD32B 0.000 2 180.00 ! CTER, Glu, *CONFIRM* +OD2C2A CD2O2A CD31C CD32C 0.000 1 0.00 ! CTER, PEML, Leu +OD2C2A CD2O2A CD31C CD32C 0.000 2 180.00 ! CTER, PEML, Leu *CONFIRM* +OD2C2A CD2O2A CD31C CD33A 0.000 1 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER +OD2C2A CD2O2A CD31C CD33A 0.000 2 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER +OD2C2A CD2O2A CD31C HDA1A 0.000 1 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER +OD2C2A CD2O2A CD31C HDA1C 0.000 1 180.00 ! CTER, PEML, pseudo-psi from ACE-CTER +OD2C2A CD2O2A CD32A CD32A 0.200 3 0.00 ! GLU, c22, chi3, old +OD2C2A CD2O2A CD32A CD32B 0.128 2 180.00 ! GLU, chi3, optimized based on propylonate, fylin 2018 +OD2C2A CD2O2A CD32A HDA2A 0.420 3 180.00 ! ASP, ACET, PEML +OD2C2A CD2O2A CD32C ND2A2 1.500 1 0.00 ! CTER, PEML, Gly +OD2C2A CD2O2A CD32C ND2A2 1.000 2 180.00 ! CTER, PEML, Gly +OD2C2A CD2O2A CD32C HDA2A 0.000 1 180.00 ! CTER, PEML, GLY +OD2C2A CD2O2A CD32C HDA2C 0.000 1 180.00 ! CTER, PEML, GLY +OD2C2A CD2O2A CD33A HDA3A 0.420 3 180.00 ! ASP, ACET, PEML +OD2C3A CD2O3A CD31A ND3P3A 0.000 1 0.00 ! CNEU/NTER +OD2C3A CD2O3A CD31C ND3P3A 0.000 1 0.00 ! CNEU/NTER +OD2C3A CD2O3A CD31A CD31A 0.900 2 180.00 ! CNEU/NTER +OD2C3A CD2O3A CD31A CD32A 0.900 2 180.00 ! CNEU/NTER +OD2C3A CD2O3A CD31A CD33A 0.400 1 0.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31A CD33A 1.400 2 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31A HDA1C 0.000 1 0.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C HDA1C 0.000 1 0.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD31A ND3P3A 0.000 1 0.00 ! CNEU/NTER +OD31F CD2O3A CD31C ND3P3A 0.000 1 0.00 ! CNEU/NTER +OD31F CD2O3A CD31A CD31A 1.500 2 0.00 ! CNEU/NTER +OD31F CD2O3A CD31A CD32A 1.500 2 0.00 ! CNEU/NTER +OD31F CD2O3A CD31A CD33A 0.400 1 180.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD31A CD33A 1.400 2 180.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD31A HDA1C 0.200 3 180.00 ! CNEU +OD31F CD2O3A CD31C HDA1C 0.200 3 180.00 ! CNEU +OD2C3A CD2O3A CD31C ND2A2 0.000 1 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C ND2A2 2.800 2 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C CD31A 0.900 2 180.00 ! CNEU/NTER +OD2C3A CD2O3A CD31C CD32A 0.900 2 180.00 ! CNEU/NTER +OD2C3A CD2O3A CD31C CD32B 0.900 2 180.00 ! PEML by analogy GLU, CNEU +OD2C3A CD2O3A CD31C CD32C 0.900 2 180.00 ! PEML by analogy ASN, CNEU +OD2C3A CD2O3A CD31C CD33A 0.400 1 0.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C CD33A 1.400 2 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD31C HDA1A 0.000 1 0.00 ! CNEU, PEML pseudo-psi +OD30C CD2O3A CD31C ND2A2 0.200 3 0.00 ! CT1, c22 +OD30C CD2O3A CD31C CD31A 0.300 1 0.00 ! CT1, PEML by analogy ILE, CT1 +OD30C CD2O3A CD31C CD31A 0.300 2 180.00 ! CT1, PEML by analogy ILE, CT1 +OD30C CD2O3A CD31C CD32A 0.300 1 0.00 ! CT1, PEML by analogy with OD30C CD2O3A CD31C CD33A +OD30C CD2O3A CD31C CD32A 0.300 2 180.00 ! CT1, PEML by analogy with OD30C CD2O3A CD31C CD33A +OD30C CD2O3A CD31C CD32B 0.300 1 0.00 ! CT1, PEML by analogy GLU, CT1 +OD30C CD2O3A CD31C CD32B 0.300 2 180.00 ! CT1, PEML by analogy GLU, CT1 +OD30C CD2O3A CD31C CD32C 0.300 1 0.00 ! CT1, PEML by analogy ASN, CT1 +OD30C CD2O3A CD31C CD32C 0.300 2 180.00 ! CT1, PEML by analogy ASN, CT1 +OD30C CD2O3A CD31C CD33A 0.300 1 0.00 ! CT1, MPO, EH 2007 +OD30C CD2O3A CD31C CD33A 0.300 2 180.00 ! CT1, MPO, EH 2007 +OD31F CD2O3A CD31C ND2A2 0.000 1 0.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD31C ND2A2 2.800 2 180.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD31C CD31A 1.500 2 0.00 ! CNEU/NTER +OD31F CD2O3A CD31C CD32A 1.500 2 0.00 ! CNEU/NTER +OD31F CD2O3A CD31C CD32B 1.500 2 0.00 ! PEML by analogy GLU, CNEU +OD31F CD2O3A CD31C CD32C 1.500 2 0.00 ! PEML by analogy ASN, CNEU +OD31F CD2O3A CD31C CD33A 0.400 1 180.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD31C CD33A 1.400 2 180.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD31C HDA1A 0.000 1 180.00 ! CNEU, PEML pseudo-psi +OD2C3A CD2O3A CD32C ND2A2 5.160 1 0.00 ! CNEU, PEML, gly +OD2C3A CD2O3A CD32C ND2A2 0.000 2 180.00 ! CNEU, PEML, gly +OD2C3A CD2O3A CD32C CD31C 0.200 3 0.00 ! ASPP, c22, chi2 +OD2C3A CD2O3A CD32C CD32B 0.200 3 0.00 ! GLUP, c22, chi2 +OD2C3A CD2O3A CD32C HDA2A 0.000 3 180.00 ! MAS, PEML 2009 +OD31F CD2O3A CD32C ND2A2 2.830 1 0.00 ! CNEU, PEML, gly +OD31F CD2O3A CD32C CD31C 0.100 1 180.00 ! ASPP/CNEU, PEML pseudo-psi +OD31F CD2O3A CD32C CD31C 0.160 2 180.00 ! ASPP/CNEU, PEML pseudo-psi +OD31F CD2O3A CD32C CD32A 0.100 1 180.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD32C CD32A 0.160 2 180.00 ! CNEU, PEML pseudo-psi +OD31F CD2O3A CD32C CD32B 0.100 1 180.00 ! GLUP, PEML pseudo-psi +OD31F CD2O3A CD32C CD32B 0.160 2 180.00 ! GLUP, PEML pseudo-psi +OD31F CD2O3A CD32C HDA2A 0.200 3 180.00 ! CNEU, gly +OD2C3A CD2O3A CD33C HDA3A 0.000 3 180.00 ! MAS, PEML 2009 *** CHANGED *** +OD30C CD2O3A CD33C HDA3A 0.000 3 180.00 ! MAS, PEML 2009 +OD31F CD2O3A CD33C HDA3A 0.000 6 180.00 ! ACEH, PEML +ND2R5A CD2R5A CD2R5A ND2R5B 14.000 2 180.00 ! IMID, imidazole +ND2R5A CD2R5A CD2R5A CD32A 3.000 2 180.00 ! HSE, c22 +ND2R5A CD2R5A CD2R5A CD33A 3.000 2 180.00 ! HSE, c22, fylin 4MIE +ND2R5A CD2R5A CD2R5A HDR5A 3.000 2 180.00 ! IMID, imidazole +ND2R5B CD2R5A CD2R5A CD32A 3.000 2 180.00 ! HSD/4MIM, 4-methyl-imidazole +ND2R5B CD2R5A CD2R5A CD33A 3.000 2 180.00 ! 4MIM, 4-methyl-imidazole +ND2R5B CD2R5A CD2R5A HDR5A 3.000 2 180.00 ! IMID, imidazole +CD32A CD2R5A CD2R5A HDR5A 2.000 2 180.00 ! HSD/4MIM, 4-methyl-imidazole +CD33A CD2R5A CD2R5A HDR5A 2.000 2 180.00 ! 4MIM, 4-methyl-imidazole +HDR5A CD2R5A CD2R5A HDR5A 2.000 2 180.00 ! IMID, imidazole +ND2R5A CD2R5A CD2R5C CD2R5C 7.800 2 180.00 ! PYRR, pyrrole +ND2R5A CD2R5A CD2R5C CD2R6D 8.190 2 180.00 ! INDO, indole +ND2R5A CD2R5A CD2R5C CD32A 3.000 2 180.00 ! TRP/INDM, methyl-indole +ND2R5A CD2R5A CD2R5C CD33A 3.000 2 180.00 ! INDM, methyl-indole +ND2R5A CD2R5A CD2R5C HDR5C 1.100 2 180.00 ! PYRR, pyrrole +HDR5A CD2R5A CD2R5C CD2R5C 3.400 2 180.00 ! PYRR, pyrrole +HDR5A CD2R5A CD2R5C CD2R6D 0.810 2 180.00 ! INDO, indole +HDR5A CD2R5A CD2R5C CD32A 4.200 2 180.00 ! TRP/INDM, methyl-indole +HDR5A CD2R5A CD2R5C CD33A 4.200 2 180.00 ! INDM, methyl-indole +HDR5A CD2R5A CD2R5C HDR5C 0.280 2 180.00 ! PYRR, pyrrole +ND2R5A CD2R5A CD32A HDA2A 0.190 3 0.00 ! HSD/4MIM, 4-methyl-imidazole +ND2R5B CD2R5A CD32A HDA2A 0.190 3 0.00 ! HSE, 4MIM, 4-methyl-imidazole +ND2R5B CD2R5A CD33A HDA3A 0.190 3 0.00 ! 4MIM +CD2R5A CD2R5A CD32A HDA2A 0.200 3 0.00 ! HSD/4MIM, 4-methyl-imidazole +ND2R5A CD2R5A CD33A HDA3A 0.190 3 0.00 ! 4MIM, 4-methyl-imidazole +CD2R5A CD2R5A CD33A HDA3A 0.000 3 0.00 ! 4MIM, 4-methyl-imidazole +CD2R5A CD2R5C CD2R5C CD2R5A 10.900 2 180.00 ! PYRR, pyrrole +CD2R5A CD2R5C CD2R5C HDR5C 3.900 2 180.00 ! PYRR, pyrrole +HDR5C CD2R5C CD2R5C HDR5C 0.700 2 180.00 ! PYRR, pyrrole +CD2R5A CD2R5C CD2R6D CD2R6A 6.610 2 180.00 ! INDO, indole +CD2R5A CD2R5C CD2R6D CD2R6D 6.340 2 180.00 ! INDO, indole +CD32A CD2R5C CD2R6D CD2R6A 3.100 2 180.00 ! TRP/INDM, methyl-indole +CD32A CD2R5C CD2R6D CD2R6D 3.100 2 180.00 ! TRP/INDM, methyl-indole +CD33A CD2R5C CD2R6D CD2R6A 3.100 2 180.00 ! INDM, methyl-indole +CD33A CD2R5C CD2R6D CD2R6D 3.100 2 180.00 ! INDM, methyl-indole +HDR5C CD2R5C CD2R6D CD2R6A 0.150 2 180.00 ! INDO, indole +HDR5C CD2R5C CD2R6D CD2R6D 0.150 2 180.00 ! INDO, indole +CD2R5A CD2R5C CD32A HDA2A 0.000 3 0.00 ! TRP/INDM, methyl-indole +CD2R6D CD2R5C CD32A HDA2A 0.000 3 0.00 ! TRP/INDM, methyl-indole +CD2R5A CD2R5C CD33A HDA3A 0.000 3 0.00 ! INDM, methyl-indole +CD2R6D CD2R5C CD33A HDA3A 0.000 3 0.00 ! INDM, methyl-indole +ND2R5C CD2R5D CD2R5D ND2R5C 14.000 2 180.00 ! IMIM, from IMID (EH) +ND2R5C CD2R5D CD2R5D CD32A 2.500 2 180.00 ! HSP, c22 +ND2R5C CD2R5D CD2R5D HDR5D 3.000 2 180.00 ! IMIM, from IMID (EH) +CD32A CD2R5D CD2R5D HDR5D 2.000 2 180.00 ! HSP/4MIM, 4-methyl-imidazole +HDR5D CD2R5D CD2R5D HDR5D 2.000 2 180.00 ! IMIM, from IMID (EH) +ND2R5C CD2R5D CD32A HDA2A 0.190 3 0.00 ! HSP, c22 +CD2R5D CD2R5D CD32A HDA2A 0.000 3 0.00 ! HSP/4MIM, 4-methyl-imidazole +OD31A CD2R6A CD2R6A CD2R6A 3.100 2 180.00 ! PHEN, phenol +OD31A CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! PHEN, phenol +OD31C CD2R6A CD2R6A CD2R6A 3.100 2 180.00 ! PHEN, phenol +OD31C CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! PHEN, phenol +CD2R6A CD2R6A CD2R6A CD2R6A 2.800 2 180.00 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6A CD2R6A CD2R6A CD2R6B 5.350 2 180.00 ! PYR, pyridine +CD2R6A CD2R6A CD2R6A CD2R6D 1.590 2 180.00 ! INDO, indole +CD2R6A CD2R6A CD2R6A CD32A 3.100 2 180.00 ! PHE/TOLU +CD2R6A CD2R6A CD2R6A CD33A 3.100 2 180.00 ! TOLU, toluene, geom + freq, peml 2005 +CD2R6A CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6B CD2R6A CD2R6A HDR6A 3.600 2 180.00 ! PYR, pyridine +CD2R6D CD2R6A CD2R6A HDR6A 1.200 2 180.00 ! INDO, indole +CD32A CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! PHE/TOLU +CD33A CD2R6A CD2R6A HDR6A 4.200 2 180.00 ! TOLU, toluene, geom + freq, peml 2005 +HDR6A CD2R6A CD2R6A HDR6A 2.400 2 180.00 ! BENZ, benzene, geom + freq, peml 2005 +CD2R6A CD2R6A CD2R6B ND2R6A 0.860 2 180.00 ! PYR, pyridine +CD2R6A CD2R6A CD2R6B CD2R6A 4.400 2 180.00 ! PYR, pyridine +CD2R6A CD2R6A CD2R6B HDR6B 5.400 2 180.00 ! PYR, pyridine +CD2R6B CD2R6A CD2R6B ND2R6B 0.810 2 180.00 ! PYRM, pyrimidine +CD2R6B CD2R6J CD2R6B ND2R6B 0.810 2 180.00 ! PYRM, pyrimidine, jal +CD2R6B CD2R6A CD2R6B HDR6B 1.380 2 180.00 ! PYRM, pyrimidine +CD2R6B CD2R6J CD2R6B HDR6B 1.380 2 180.00 ! PYRM, pyrimidine, jal +CD2R6H CD2R6J CD2R6B ND2B1 2.000 2 180.00 ! CYT, jal +CD2R6H CD2R6J CD2R6B ND2R6B 0.800 2 180.00 ! CTT/PYRM, pyrimidine, jal +HDR6A CD2R6J CD2R6B ND2B1 2.000 2 180.00 ! CYT, jal +HDR6A CD2R6A CD2R6B ND2R6A 1.200 2 180.00 ! PYR, pyridine +HDR6A CD2R6A CD2R6B ND2R6B 3.420 2 180.00 ! PYRM, pyrimidine +HDR6A CD2R6J CD2R6B ND2R6B 3.420 2 180.00 ! PYRM, pyrimidine, jal +HDR6A CD2R6A CD2R6B HDR6B 2.400 2 180.00 ! PYR, pyridine +CD2R6A CD2R6A CD2R6D ND2R5A 1.930 2 180.00 ! INDO, indole +CD2R6A CD2R6A CD2R6D CD2R5C 1.680 2 180.00 ! INDO, indole +CD2R6A CD2R6A CD2R6D CD2R6D 1.340 2 180.00 ! INDO, indole +HDR6A CD2R6A CD2R6D ND2R5A 0.920 2 180.00 ! INDO, indole +HDR6A CD2R6A CD2R6D CD2R5C 0.440 2 180.00 ! INDO, indole +HDR6A CD2R6A CD2R6D CD2R6D 0.920 2 180.00 ! INDO, indole +HDR6A CD2R6J CD2R6F ND2R6B 2.800 2 180.00 ! CYT/PYRM, pyrimidine, jal +CD2O4A CD2R6J CD2R6H ND2R6B 3.000 2 180.00 ! THY, jal +CD2O4A CD2R6J CD2R6H ND2R6C 3.000 2 180.00 ! THY, jal +CD2O4A CD2R6J CD2R6H HDR6B 1.000 2 180.00 ! THY, jal +CD2R6B CD2R6J CD2R6H ND2R6B 0.800 2 180.00 ! CYT/PYRM, pyrimidine, jal +CD2R6B CD2R6J CD2R6H ND2R6C 0.800 2 180.00 ! CYT, jal +CD2R6B CD2R6J CD2R6H HDR6B 4.200 2 180.00 ! CYT/PYRM, pyrimidine, jal +CD33A CD2R6J CD2R6H ND2R6B 5.600 2 180.00 ! THY, jal +CD33A CD2R6J CD2R6H ND2R6C 5.600 2 180.00 ! THY, jal +CD33A CD2R6J CD2R6H HDR6B 1.000 2 180.00 ! THY, jal +HDR6A CD2R6J CD2R6H ND2R6B 2.800 2 180.00 ! CYT/PYRM, pyrimidine, jal +HDR6A CD2R6J CD2R6H ND2R6C 2.800 2 180.00 ! CYT, jal +HDR6A CD2R6J CD2R6H HDR6B 2.400 2 180.00 ! CYT/PYR, pyridine, jal +CD2R6A CD2R6A CD32A HDA2A 0.000 6 0.00 ! PHE/TOLU +CD2O4A CD2R6J CD33A HDA3A 0.460 3 0.00 ! THY, jal +CD2R6A CD2R6A CD33A HDA3A 0.000 6 0.00 ! TOLU, toluene, geom + freq, peml 2005 +CD2R6H CD2R6J CD33A HDA3A 0.460 3 0.00 ! THY, jal +HDR6A CD2R6A CD33A HDA3A 0.000 6 0.00 ! TOLU, toluene, geom + freq, peml 2005 +HDR6A CD2R6J CD33A HDA3A 0.000 6 0.00 ! TOLU, toluene, geom + freq, peml 2005, jal +ND2R6B CD2R6B CD2R6F ND2R5A 7.600 2 180.00 ! PUR0, purine, butterfly mode +ND2R6B CD2R6B CD2R6F ND2R5B 7.600 2 180.00 ! PUR1, purine, butterfly mode +ND2R6B CD2R6B CD2R6F CD2R6F 0.100 2 180.00 ! PUR0/1, purine +HDR6B CD2R6B CD2R6F ND2R5A 2.000 2 180.00 ! PUR1, purine, tautomer A, imidazole ring +HDR6B CD2R6B CD2R6F ND2R5B 2.000 2 180.00 ! PUR0, purine, tautomer B, imidazole ring +HDR6B CD2R6B CD2R6F CD2R6F 0.100 2 180.00 ! PUR0/1, purine, imidazole ring +ND2B1 CD2R6C CD2R6F ND2R5E 0.000 2 180.00 ! ADE, cmb 04/10 +ND2B1 CD2R6C CD2R6F CD2R6F 4.000 2 180.00 ! ADE, cmb 04/10 +ND2R6B CD2R6C CD2R6F ND2R5E 2.500 2 180.00 ! ADE, butterfly motion, jal +ND2R6B CD2R6C CD2R6F CD2R6F 1.800 2 180.00 ! ADE, cmb 04/10 +ND2R5A CD2R6D CD2R6D CD2R5C 8.500 2 180.00 ! INDO, indole +ND2R5A CD2R6D CD2R6D CD2R6A 1.610 2 180.00 ! INDO, indole +CD2R5C CD2R6D CD2R6D CD2R6A 1.760 2 180.00 ! INDO, indole +CD2R6A CD2R6D CD2R6D CD2R6A 3.460 2 180.00 ! INDO, indole +ND2R5A CD2R6F CD2R6F ND2R5B 5.100 2 180.00 ! PUR0/1, purine, imidazole ring +ND2R5A CD2R6F CD2R6F ND2R6B 12.500 2 180.00 ! PUR0, purine, butterfly mode +ND2R5A CD2R6F CD2R6F CD2R6B 12.500 2 180.00 ! PUR1, purine, butterfly mode +ND2R5B CD2R6F CD2R6F ND2R6B 12.500 2 180.00 ! PUR1, purine, butterfly mode +ND2R5B CD2R6F CD2R6F CD2R6B 12.500 2 180.00 ! PUR0, purine, butterfly mode +ND2R5E CD2R6F CD2R6F ND2R6B 12.500 2 180.00 ! GUA, cmb 04/10 +ND2R6B CD2R6F CD2R6F CD2R6B 0.100 2 180.00 ! PUR0/1, purine +ND2R5E CD2R6F CD2R6F ND2R5D 14.000 2 180.00 ! ADE, cmb 04/10 +ND2R5D CD2R6F CD2R6F CD2O4A 0.000 2 180.00 ! GUA, jal +ND2R5D CD2R6F CD2R6F CD2R6C 3.000 2 180.00 ! ADE, va A; butterfly motion, cmb 04/10 +ND2R6B CD2R6F CD2R6F CD2O4A 2.000 2 180.00 ! GUA, jal +ND2R6B CD2R6F CD2R6F CD2R6C 2.000 2 180.00 ! ADE, cmb 04/10 +CD32A ND2R5D CD2R6F ND2R6B 1.000 2 180.00 ! va; Et-Gua +CD32A ND2R5D CD2R6F CD2R6F 1.000 2 180.00 ! va; Et-Gua +CD32A ND2R5D CD2R5F ND2R5E 1.000 2 180.00 ! va; Et-Gua, jal +CD32A ND2R5D CD2R5F HDR5B 1.000 2 180.00 ! va; Et-Gua, jal +CD33A CD32A ND2R5D CD2R6F 1.000 3 0.00 ! va; Et-Gua +HDA2A CD32A ND2R5D CD2R6F 0.000 3 0.00 ! va; Et-Gua +HDA2A CD32A ND2R5D CD2R5F 0.000 3 0.00 ! va; Et-Gua, jal +CD33A CD32A ND2R5D CD2R5F 1.000 3 0.00 ! va; Et-Gua, jal +ND2R5D CD32A CD33A HDA3A 0.160 3 0.00 ! va; Et-Gua +CD31A CD30A CD32A HDA2A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD32A CD30A CD32A HDA2A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD32A CD30A CD32A HDA3A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD33A CD30A CD32A HDA2A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD31A CD30A CD33A HDA3A 0.200 3 0.00 ! NEOP, nopentane, 3/92 +CD32A CD30A CD33A HDA3A 0.200 3 0.00 ! NEOP, nopentane, alkane, 3/92 - cmb, needs test +CD33A CD30A CD33A HDA3A 0.200 3 0.00 ! NEOP, nopentane, alkane, 3/92 +CD33A CD315B CD315B CD33A 0.200 3 0.00 ! THF, cmb +OD305A CD315B CD325B CD325B 0.000 3 0.00 ! TF2M, cmb +OD305A CD315B CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +CD325B CD315B CD325B CD325B 0.410 3 180.00 ! TF2M, cmb +CD325B CD315B CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +CD33A CD315B CD325B CD325B 0.200 3 0.00 ! TF2M, cmb +CD33A CD315B CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +HDA1R5 CD315B CD325B CD325B 0.200 3 0.00 ! TF2M, cmb +HDA1R5 CD315B CD325B HDA2R5 0.200 3 0.00 ! TF2M, cmb +OD305A CD315B CD33A HDA3A 0.200 3 0.00 ! TF2M, cmb +CD325B CD315B CD33A HDA3A 0.200 3 0.00 ! TF2M, cmb +CD325A CD315A CD33A HDA3A 0.200 3 0.00 ! CPNM, cmb +HDA1R5 CD315B CD33A HDA3A 0.200 3 0.00 ! TF2M, cmb +HDA1R5 CD315A CD33A HDA3A 0.200 3 0.00 ! CPNM, cmb +ND3P3A CD31C CD31A CD33A 0.550 1 180.00 ! ILE/VAL, chi1, Xiao, NTER +ND3P3A CD31C CD31A CD33A 0.230 2 0.00 ! ILE/VAL, chi1, Xiao, NTER +ND3P3A CD31C CD31A CD33A 0.540 3 0.00 ! ILE/VAL, chi1, Xiao, NTER +ND3P3A CD31A CD31A HDA1A 0.000 1 0.00 ! NTER +ND3P3A CD31C CD31A HDA1A 0.000 1 0.00 ! NTER +OD31A CD31A CD31A CD2O1A 0.200 3 0.00 ! THR, c22, chi1, WHAT IS THIS? +OD31A CD31A CD31A HDA1C 0.075 3 0.00 ! THR/BUO2, NTER +CD2O1A CD31A CD31A HDA1A 0.200 3 0.00 ! NTER +CD2O2A CD31A CD31A CD33A 0.200 3 0.00 ! CTER +CD2O2A CD31A CD31A HDA1A 0.200 3 0.00 ! CTER +CD2O3A CD31A CD31A CD33A 0.200 3 0.00 ! CNEU +CD2O3A CD31A CD31A HDA1A 0.200 3 0.00 ! CNEU +CD31A CD31A CD31A HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD32A CD31A CD31A HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD33A CD31A CD31A HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD33A CD31A CD31A HDA1C 0.200 3 0.00 ! NTER +CD33A CD31A CD31C HDA1C 0.200 3 0.00 ! NTER +HDA1A CD31A CD31A HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD31A HDA1C 0.200 3 0.00 ! NTER +HDA1A CD31A CD31C HDA1C 0.200 3 0.00 ! NTER +OD31A CD31A CD31C HDA1A 0.075 3 0.00 ! THR/BUO2 +CD31A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER +OD31A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER - Thr, jing +CD31A CD32A CD31C CD2O2A 0.200 3 0.00 ! CTER, zhu +CD31A CD31A CD31C CD2O3A 0.200 3 0.00 ! CNEU +CD32A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER +CD32A CD31A CD31C CD2O3A 0.200 3 0.00 ! CNEU +CD32A CD31A CD31C HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +CD33A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER, VAL +CD33A CD31A CD31C CD2O3A 0.200 3 0.00 ! CNEU +CD33A CD31A CD31C HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +HDA1A CD31A CD31C ND2A2 0.200 3 0.00 ! ILE/VAL, alkanes +HDA1A CD31A CD31C CD2O1A 0.200 3 0.00 ! ILE/VAL, alkanes +HDA1A CD31A CD31C CD2O2A 0.200 3 0.00 ! CTER +HDA1A CD31A CD31C CD2O3A 0.200 3 0.00 ! CNEU +HDA1A CD31A CD31C HDA1A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +ND3P2A CD31A CD32A HDA2A 0.000 1 0.00 ! NTER +ND3P2A CD31C CD32A HDA2A 0.000 1 0.00 ! NTER +ND3P3A CD31A CD32A HDA2A 0.000 1 0.00 ! NTER +ND3P3A CD31C CD32A HDA2A 0.000 1 0.00 ! NTER +ND3P3A CD31C CD32B HDA2A 0.000 1 0.00 ! NTER, PEML by analogy for GLU +ND3P3A CD31C CD32C HDA2A 0.000 1 0.00 ! NTER, PEML by analogy for ASN +ND3P3A CD31C CD32A CD32C 0.200 3 0.00 ! NTER +ND3P3A CD31C CD32A CD2R5A 0.200 3 0.00 ! NTER, PEML by analogy for HSD +ND3P3A CD31C CD32A CD2R5C 0.200 3 0.00 ! NTER, PEML by analogy for TRP +ND3P3A CD31C CD32A CD2R5D 0.200 3 0.00 ! NTER, PEML by analogy for HSP +ND3P3A CD31C CD32A CD2R6A 0.200 3 0.00 ! NTER, PEML by analogy for PHE +ND3P3A CD31C CD31A CD32A 0.200 3 0.00 ! NTER, PEML by analogy for ILE +ND3P3A CD31C CD32A CD31A 0.200 3 0.00 ! NTER, PEML by analogy for LEU +ND3P3A CD31C CD32B CD32A 0.200 3 0.00 ! NTER, PEML by analogy for GLU +ND3P3A CD31C CD32B CD32C 0.200 3 0.00 ! NTER, alex by analogy for GLUP +ND3P3A CD31C CD32A CD2O2A 0.200 3 0.00 ! NTER - ASP, jing +OD31A CD31A CD32A CD33A 0.200 1 0.00 ! BUO2, 2-butanol +OD31A CD31A CD32A CD33A 0.410 2 0.00 ! BUO2, 2-butanol +OD31A CD31A CD32A CD33A 0.400 3 0.00 ! BUO2, 2-butanol +OD31A CD31A CD32A CD32A 0.200 1 0.00 ! PEO2, 2-pentanol, cmb - needs test +OD31A CD31A CD32A CD32A 0.410 2 0.00 ! PEO2, 2-pentanol, cmb - needs test +OD31A CD31A CD32A CD32A 0.400 3 0.00 ! PEO2, 2-pentanol, cmb - needs test +OD31A CD31A CD32A HDA2A 0.075 3 0.00 ! BUO2, 2-butanol +CD2O1A CD31A CD32A HDA2A 0.200 3 0.00 ! NTER +CD2O2A CD31A CD32A CD32C 0.200 3 0.00 ! CTER +CD2O2A CD31C CD32A CD32C 0.200 3 0.00 ! GLUP +CD2O3A CD31C CD32B CD32C 0.200 3 0.00 ! GLUP +CD2O2A CD31A CD32A HDA2A 0.200 3 0.00 ! CTER +CD2O3A CD31A CD32A CD32C 0.200 3 0.00 ! CNEU +CD2O3A CD31C CD32A CD32C 0.200 3 0.00 ! GLUP +CD2O3A CD31C CD32A CD2R5C 0.200 3 0.00 ! PEML by analogy TRP +CD2O3A CD31A CD32A HDA2A 0.200 3 0.00 ! CNEU +CD31A CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD31C CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +CD32A CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD33A CD31A CD31A CD33A 0.126 2 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD31A CD33A 0.084 3 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD31A CD33A 0.144 4 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD31A CD33A 0.200 5 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD32A 0.126 2 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD32A 0.084 3 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD32A 0.144 4 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD32A 0.200 5 0.00 ! from alkane, Igor 3/26/2005, cmb - needs test +CD33A CD31A CD32A CD33A 0.126 2 0.00 ! alkane, Igor 3/26/2005 +CD33A CD31A CD32A CD33A 0.084 3 0.00 ! alkane, Igor 3/26/2005 +CD33A CD31A CD32A CD33A 0.144 4 0.00 ! alkane, Igor 3/26/2005 +CD33A CD31A CD32A CD33A 0.200 5 0.00 ! alkane, Igor 3/26/2005 +CD33A CD30A CD32A CD33A 0.126 2 0.00 ! cmb, from alkane, Igor 3/26/2005 - needs test +CD33A CD30A CD32A CD33A 0.084 3 0.00 ! cmb, from alkane, Igor 3/26/2005 - needs test +CD33A CD30A CD32A CD33A 0.144 4 0.00 ! cmb, from alkane, Igor 3/26/2005 - needs test +CD33A CD30A CD32A CD33A 0.200 5 0.00 ! cmb, from alkane, Igor 3/26/2005 - needs test +CD33A CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD32A CD31A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD32A CD31C 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +HDA1A CD31A CD32A CD32A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD32A CD33A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD31A CD32A HDA2A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1C CD31A CD32A CD32A 0.200 3 0.00 ! NTER +HDA1C CD31A CD32A CD32C 0.200 3 0.00 ! NTER +HDA1C CD31C CD32A CD32C 0.200 3 0.00 ! NTER +HDA1C CD31C CD32A CD2R5A 0.200 3 0.00 ! NTER, PEML by analogy HSD +HDA1C CD31C CD32A CD2R5C 0.200 3 0.00 ! NTER, PEML by analogy TRP +HDA1C CD31C CD32A CD2R5D 0.200 3 0.00 ! NTER, PEML by analogy HSP +HDA1C CD31C CD32A CD2R6A 0.200 3 0.00 ! NTER, PEML by analogy PHE +HDA1C CD31C CD32A CD2O2A 0.200 3 0.00 ! NTER - ASP, jing +HDA1C CD31A CD32A HDA2A 0.200 3 0.00 ! NTER +ND3P3A CD31A CD33A HDA3A 0.000 1 0.00 ! CNEU/NTER, NTER-CT3 %% +ND3P3A CD31C CD33A HDA3A 0.000 1 0.00 ! CNEU/NTER, NTER-CT3 %% +OD31A CD31A CD33A HDA3A 0.075 3 0.00 ! PRO2, 2-propanol +CD2O1A CD31A CD33A HDA3A 0.200 3 0.00 ! NTER, IBUT, isobutane, 3/92 +CD2O2A CD31A CD33A HDA3A 0.200 3 0.00 ! CTER, zwitterionic amino acid +CD2O3A CD31A CD33A HDA3A 0.200 3 0.00 ! CNEU +CD31A CD31A CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD31C CD31A CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +CD32A CD31A CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +CD33A CD31A CD33A HDA3A 0.150 3 0.00 ! IBUT, isobutane, 10/07, va +HDA1A CD31A CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 +HDA1A CD316A CD33A HDA3A 0.200 3 0.00 ! CHXM, from IBUT, 3/92, cmb 12/09 +HDA1C CD31A CD33A HDA3A 0.200 3 0.00 ! CNEU/NTER, IBUT, isobutane, 3/92 *DELETE* +HDA1C CD31C CD33A HDA3A 0.200 3 0.00 ! CNEU/NTER, IBUT, isobutane, 3/92 *DELETE* +ND2A2 CD31C CD32A SD30B 0.200 3 0.00 ! DISU, chi1, c22 +ND2A2 CD31C CD32A HDA2A 0.200 3 0.00 ! GLN, alkanes +ND2A2 CD31C CD32B HDA2A 0.200 3 0.00 ! GLU, from ND2A2 CD31C CD32A HDA2A +ND3A3 CD31C CD32A CD32A 0.800 1 0.00 ! PRO FIT PES PEML CHI1 +ND3A3 CD31C CD32A CD32A 2.800 2 0.00 ! PRO FIT PES PEML CHI1 +ND3A3 CD31C CD32A CD32A 1.100 3 0.00 ! PRO FIT PES PEML CHI1 +ND3A3 CD31C CD32A HDA2A 0.200 3 0.00 ! PRO +OD30C CD31C CD32A HDA2A 0.190 3 0.00 ! EAS/Lipid-H, charmm27 +OD30C CD31C CD32B HDA2A 0.190 3 0.00 ! EAS/Lipid-H, charmm27 +CD2O1A CD31C CD32A SD30B 0.200 3 0.00 ! DISU, chi1, c22 +CD2O1A CD31C CD32A HDA2A 0.200 3 0.00 ! GLN, alkanes +CD2O1A CD31C CD32B HDA2A 0.200 3 0.00 ! GLU, from CD2O1A CD31C CD32A HDA2A +CD2O2A CD31C CD32A SD31B 0.200 3 0.00 ! CTER, terminal Cys +CD2O3A CD31C CD32A SD31B 0.200 3 0.00 ! PEML by analogy CYS, CNEU +CD2O2A CD31C CD32A CD2R5C 0.200 3 0.00 ! TRP/CTER, PEML +CD2O2A CD31C CD32A CD2R5D 0.200 3 0.00 ! CTER, PEML, HSE +CD2O2A CD31C CD32A CD2R5A 0.200 3 0.00 ! CTER, PEML, HSD +CD2O3A CD31C CD32A CD2R5A 0.200 3 0.00 ! CNEU, PEML, HSD +CD2O3A CD31C CD32A CD2R5D 0.200 3 0.00 ! CNEU, PEML, HSP +CD2O2A CD31C CD32A CD32A 0.200 3 0.00 ! CTER +CD2O3A CD31C CD32A CD31A 0.200 3 0.00 ! CNEU, PEML by analogy LEU +CD2O3A CD31C CD32A CD32A 0.200 3 0.00 ! CNEU, PEML by analogy with CD2O2A CD31C CD32A CD32A +CD2O3A CD31C CD32B CD32A 0.200 3 0.00 ! CNEU, PEML by analogy GLU +CD2O2A CD31C CD32B CD32A 0.200 3 0.00 ! CTER, Glu +CD2O2A CD31C CD32B CD32C 0.200 3 0.00 ! CTER, GLUP +CD2O2A CD31C CD32A HDA2A 0.200 3 0.00 ! CTER +CD2O2A CD31C CD32B HDA2A 0.200 3 0.00 ! CTER, Glu +CD2O3A CD31C CD32A HDA2A 0.200 3 0.00 ! CNEU +HDA1A CD31C CD32A OD31A 0.270 1 0.00 ! SER/PRO1, 1-propanol +HDA1A CD31C CD32A OD31A 0.050 2 0.00 ! SER/PRO1, 1-propanol +HDA1A CD31C CD32A OD31A 0.120 3 0.00 ! SER/PRO1, 1-propanol +HDA1A CD31C CD32A SD30B 0.190 3 0.00 ! DISU, c22 +HDA1A CD31C CD32A SD31B 0.120 3 0.00 ! CYS/PRSH +HDA1C CD31C CD32A SD31B 0.120 3 0.00 ! PEML by analogy CYS, CTER +HDA1A CD31C CD32A CD2O2A 0.200 3 0.00 ! ASP, c22 +HDA1A CD31C CD32A CD2R5A 0.190 3 0.00 ! HSD, alkanes +HDA1A CD31C CD32A CD2R5C 0.200 3 0.00 ! TRP, alkanes +HDA1A CD31C CD32A CD2R5D 0.190 3 0.00 ! HSP, alkanes +HDA1A CD31C CD32A CD2R6A 0.040 3 0.00 ! PHE, c22 +HDA1A CD31C CD32A CD31A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +HDA1A CD31C CD32A CD32A 0.190 3 0.00 ! LYS +HDA1A CD31C CD32B CD32A 0.190 3 0.00 ! GLU, from HDA1A CD31C CD32A CD32A +HDA1A CD31C CD32B CD32C 0.190 3 0.00 ! GLUP, from HDA1A CD31C CD32A CD32A +HDA1A CD31C CD32A CD32C 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +HDA1A CD31C CD32A HDA2A 0.200 3 0.00 ! GLN, IBUT, isobutane, 3/92 +HDA1A CD31C CD32B HDA2A 0.200 3 0.00 ! GLU, from HDA1A CD31C CD32A HDA2A +ND2A2 CD31C CD32C CD2O3A 0.200 3 0.00 ! ASPP, c22, chi1 +ND2A2 CD31C CD32C HDA2A 0.200 3 0.00 ! ASN, alkanes +CD2O1A CD31C CD32C CD2O3A 0.200 3 0.00 ! GLUP, c22, chi1 +CD2O1A CD32C CD31C CD2O3A 0.200 3 0.00 ! PEML by analogy ASN, CNEU +CD2O1A CD31C CD32C HDA2A 0.200 3 0.00 ! ASN, alkanes +CD2O2A CD31C CD32C CD2O1A 0.200 3 0.00 ! CTER, ASN +CD2O2A CD31C CD32A CD2O2A 0.200 3 0.00 ! PEML by analogy CTER, ASP +CD2O2A CD31C CD32A CD2R6A 0.200 3 0.00 ! PEML by analogy CTER, PHE +CD2O3A CD31C CD32A CD2O2A 0.200 3 0.00 ! PEML by analogy CNEU, ASP +CD2O2A CD31C CD32C HDA2A 0.200 3 0.00 ! CTER +HDA1A CD31C CD32C CD2O1A 0.200 3 0.00 ! ASN, alkanes +HDA1A CD31C CD32C CD2O3A 0.200 3 0.00 ! ASPP/GLUP, c22 +HDA2A CD32B CD31C CD2O3A 0.200 3 0.00 ! PEML by analogy GLU, CNEU +HDA2A CD32C CD31C CD2O3A 0.200 3 0.00 ! PEML by analogy ASN, CNEU +ND2A2 CD31C CD33A HDA3A 0.040 3 0.00 ! ALAD +OD30C CD31C CD33A HDA3A 0.160 3 0.00 ! EAS, charmm27 +CD2O1A CD31C CD33A HDA3A 0.870 3 0.00 ! ALAD +CD2O2A CD31C CD33A HDA3A 0.200 3 0.00 ! CTER +CD2O3A CD31C CD33A HDA3A 0.200 3 0.00 ! CNEU +HDA1A CD31C CD33A HDA3A 0.200 3 0.00 ! IBUT, isobutane, 3/92 ADDED FOR ALAD +CD325A CD325A CD325A CD325A 0.410 3 180.00 ! CPEN, cyclopentane, viv 10/4/05 +CD325A CD315A CD325A CD325A 0.410 3 180.00 ! CPNM, cmb +CD315A CD325A CD325A CD325A 0.410 3 180.00 ! CPNM, cmb +CD325A CD325A CD325A CD33A 0.160 3 0.00 ! CPEN, viv +CD325A CD325A CD315A CD33A 0.160 3 0.00 ! CPNM, cmb +CD325A CD325A CD315A OD31A 0.160 3 0.00 ! CPO1, cmb, needs test +CD325A CD325A CD325A HDA2R5 0.160 3 0.00 ! CPEN, viv +CD325A CD325A CD315A HDA1R5 0.160 3 0.00 ! CPNM, cmb +CD315A CD325A CD325A HDA2R5 0.160 3 0.00 ! CPNM, cmb +CD325A CD315A CD325A HDA2R5 0.160 3 0.00 ! CPNM, cmb +CD33A CD325A CD325A CD33A 0.160 3 0.00 ! CPEN, cyclopentane, viv +CD33A CD315A CD325A HDA2R5 0.160 3 0.00 ! CPNM, cmb +OD31A CD315A CD325A HDA2R5 0.160 3 0.00 ! CPO1, cmb +CD33A CD325A CD325A HDA2R5 0.160 3 0.00 ! CPEN, viv +HDA2R5 CD325A CD325A HDA2R5 0.160 3 0.00 ! CPEN, viv +HDA1R5 CD315A CD325A HDA2R5 0.160 3 0.00 ! CPNM, cmb +OD305A CD325B CD325B CD325B 0.000 3 0.00 ! THF, viv +OD305A CD325B CD325B HDA2R5 0.190 3 0.00 ! THF viv +CD315B CD325B CD325B CD325B 0.410 3 180.00 ! TF2M, cmb +CD315B CD325B CD325B HDA2R5 0.190 3 0.00 ! TF2M, cmb +CD325B CD325B CD325B CD325B 0.410 3 180.00 ! THF, viv +CD325B CD325B CD325B HDA2R5 0.190 3 0.00 ! THF, viv +HDA2R5 CD325B CD325B HDA2R5 0.190 3 0.00 ! THF, viv +CD316A CD326A CD326A CD326A 0.073 1 0.00 ! CHXM, from CD32A, 9/09, cmb +CD316A CD326A CD326A CD326A 0.043 2 0.00 ! CHXM, from CD32A, 9/09, cmb +CD316A CD326A CD326A CD326A 0.119 3 180.00 ! CHXM, from CD32A, 9/09, cmb +CD316A CD326A CD326A CD326A 0.098 4 0.00 ! CHXM, from CD32A, 9/09, cmb +CD316A CD326A CD326A CD326A 0.046 5 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.073 1 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.043 2 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.119 3 180.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.098 4 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD316A CD326A CD326A 0.046 5 0.00 ! CHXM, from CD32A, 9/09, cmb +!to be checked +CD326A CD326A CD326A CD326A 0.073 1 0.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.043 2 0.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.119 3 180.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.098 4 0.00 ! CHEX, from CD32A, 9/09, cmb +CD326A CD326A CD326A CD326A 0.046 5 0.00 ! CHEX, from CD32A, 9/09, cmb +! +CD326A CD326A CD316A CD33A 0.073 1 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.043 2 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.119 3 180.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.098 4 0.00 ! CHXM, from CD32A, 9/09, cmb +CD326A CD326A CD316A CD33A 0.046 5 0.00 ! CHXM, from CD32A, 9/09, cmb +CD33A CD316A CD326A HDA2A 0.190 3 0.00 ! CHXM, from CD32A, 12/09, cmb +CD326A CD326A CD316A HDA1A 0.190 3 0.00 ! CHXM, from CD32A, 12/09, cmb +CD316A CD326A CD326A HDA2A 0.190 3 0.00 ! CHXM, from CD32A, 12/09, cmb +CD326A CD316A CD326A HDA2A 0.190 3 0.00 ! CHXM, from CD32A, 12/09, cmb +CD326A CD326A CD326A HDA2A 0.190 3 0.00 ! CHEX, from CD32A, 9/09, cmb +HDA1A CD316A CD326A HDA2A 0.190 3 0.00 ! CHXM, from CD32A, 9/09, cmb +HDA2A CD326A CD326A HDA2A 0.190 3 0.00 ! CHEX, from CD32A, 9/09, cmb +OD306A CD326B CD326B CD326B 0.19225 1 180.00 ! THP, sng 1/06 +OD306A CD326B CD326B CD326B 1.00000 2 180.00 ! THP, sng 1/06 +OD306A CD326B CD326B CD326B 0.59457 3 0.00 ! THP, sng 1/06 +OD306A CD326B CD326B CD326B 0.07862 4 180.00 ! THP, sng 1/06 +OD306A CD326B CD326B OD306A 0.19225 1 180.00 ! DIOX, from THP, sng 1/06, cmb - needs test +OD306A CD326B CD326B OD306A 1.00000 2 180.00 ! DIOX, from THP, sng 1/06, cmb - needs test +OD306A CD326B CD326B OD306A 0.59457 3 0.00 ! DIOX, from THP, sng 1/06, cmb - needs test +OD306A CD326B CD326B OD306A 0.07862 4 180.00 ! DIOX, from THP, sng 1/06, cmb - needs test +OD306A CD326B CD326B HDA2E 0.190 3 0.00 ! THP, viv +CD326B CD326B CD326B CD326B 0.498 2 0.00 ! THP, sng cyclohexane 2/06 +CD326B CD326B CD326B CD326B 0.59844 3 180.00 ! THP, sng cyclohexane 2/06 +CD326B CD326B CD326B CD326B 0.41746 4 0.00 ! THP, sng cyclohexane 2/06 +CD326B CD326B CD326B CD326B 0.24829 5 180.00 ! THP, sng cyclohexane 2/06 +CD326B CD326B CD326B CD33A 0.190 3 0.00 ! THP, viv +CD326B CD326B CD326B HDA2E 0.190 3 0.00 ! THP, viv +CD33A CD326B CD326B CD33A 0.190 3 0.00 ! THP, tetrahydropyran, viv +CD33A CD326B CD326B HDA2E 0.190 3 0.00 ! THP, viv +HDA2E CD326B CD326B HDA2E 0.190 3 0.00 ! THP, viv +OD306A CD326B CD33A HDA3A 0.160 3 0.00 ! Methyl-THP, viv +CD326B CD326B CD33A HDA3A 0.160 3 0.00 ! Methyl-THP, viv +HDA2E CD326B CD33A HDA3A 0.160 3 0.00 ! Methyl-THP, viv +ND2P1A CD32A CD32A CD32A 0.457 1 180.00 ! RMSE = 0.121553, mguan24, fylin +ND2P1A CD32A CD32A CD32A 0.400 2 0.00 ! RMSE = 0.121553, fylin +ND2P1A CD32A CD32A CD32A 0.254 3 0.00 ! RMSE = 0.121553, fylin +ND2P1A CD32A CD32A HDA2A 0.190 3 0.00 ! ARG, c22 +ND2A2 CD32C CD32A CD32A 0.500 1 180.00 ! Ac-LYS, jal +ND2A2 CD32C CD32A CD32A 0.375 2 0.00 ! Ac-LYS, jal +ND2A2 CD32C CD32A CD32A 0.250 3 0.00 ! Ac-LYS, jal +ND3A3 CD32A CD32A CD32A 2.100 1 0.00 ! PRO FIT PES PEML CHI3 +ND3A3 CD32A CD32A CD32A 0.800 2 0.00 ! PRO FIT PES PEML CHI3 +ND3A3 CD32A CD32A CD32A 0.600 3 0.00 ! PRO FIT PES PEML CHI3 +ND3A3 CD32A CD32A HDA2A 0.200 3 0.00 ! PRO +ND3P3A CD32A CD32A OD31A 1.000 1 180.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32A CD32A OD31A 0.500 2 0.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P3A CD32A CD32A OD31A 0.500 3 0.00 ! ETAM, alpha5, qm, EH 2007 (chk pe) +ND3P2A CD32A CD32A OD31A 2.750 1 0.00 ! CHOL, Lipid-a5 (oct. 09 EH), lipid +ND3P2A CD32A CD32A OD31A 0.750 2 0.00 ! CHOL, Lipid-a5 (oct. 09 EH) +ND3P2A CD32A CD32A OD31A 0.000 3 0.00 ! CHOL, Lipid-a5 (oct. 09 EH) +ND3P2A CD32A CD32A HDA2A 0.190 3 0.00 ! CHOL, charmm27, ammonium cation +ND3P3A CD32A CD32A HDA2A 0.190 3 0.00 ! ETAM, charmm27, ammonium cation +ND3P3A CD32A CD32A CD32A 0.328 1 180.00 ! RMSE = 0.089528 for LYS chi4 optimized feb6, fylin +ND3P3A CD32A CD32A CD32A 0.565 2 0.00 ! RMSE = 0.089528 for LYS chi4 optimized feb6, fylin +ND3P3A CD32A CD32A CD32A 0.546 3 0.00 ! RMSE = 0.089528 for LYS chi4 optimized feb6, fylin +ND3P2A CD31C CD32A CD32A 0.200 3 0.00 ! LYS, chi4 +ND3P2A CD32A CD32A CD32A 0.200 3 0.00 ! LYS, chi4 +OD30A CD32A CD32A OD30A 0.3681 1 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 1.2036 2 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 0.1171 3 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 0.1612 4 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 0.0340 5 0.00 ! DMOE, viv +OD30A CD32A CD32A OD30A 0.0225 6 0.00 ! DMOE, viv +OD30A CD32A CD32A CD32A 0.160 1 180.00 ! MPE, ATM +OD30A CD32A CD32A CD32A 0.390 2 0.00 ! MPE, ATM +OD30A CD32A CD32A CD33A 0.160 1 180.00 ! MPE, methylpropylether, 2/12/05, ATM +OD30A CD32A CD32A CD33A 0.390 2 0.00 ! MPE, ATM +OD30A CD32A CD32A HDA2A 0.190 3 0.00 ! DEET, diethylether alex +OD30B CD32A CD32A HDA2A 0.190 3 0.00 ! CHOL, charmm27, ammonium cation +OD30B CD32A CD32A HDA2C 0.190 3 0.00 ! CHOL, charmm27, ammonium cation +HDA1A CD31C CD32A OD30B 0.200 3 0.00 ! GLYC +HDA1A CD31C CD32B OD30B 0.200 3 0.00 ! GLYP +HDP1A OD30B CD32A CD32A 0.140 3 0.00 ! CHOL, charmm27 +HDP1A OD30B CD32A HDA2A 0.140 3 0.00 ! CHOL, charmm27 +OD31B CD32A CD32A CD32A 0.200 1 0.00 ! BUO1, 1-butanol +OD31B CD32A CD32A CD32A 0.410 2 0.00 ! BUO1, 1-butanol +OD31B CD32A CD32A CD32A 0.400 3 0.00 ! BUO1, 1-butanol +OD31B CD32A CD32A CD31A 0.200 1 0.00 ! B3MO1 from BUO1, cmb needs test +OD31B CD32A CD32A CD31A 0.410 2 0.00 ! B3MO1 from BUO1, cmb needs test +OD31B CD32A CD32A CD31A 0.400 3 0.00 ! B3MO1 from BUO1, cmb needs test +OD31B CD32A CD32A CD33A 0.200 1 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A CD33A 0.410 2 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A CD33A 0.400 3 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A HDA2A 0.270 1 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A HDA2A 0.050 2 0.00 ! PRO1, 1-propanol +OD31B CD32A CD32A HDA2A 0.120 3 0.00 ! PRO1, 1-propanol +SD30A CD32A CD32A HDA2A 0.139 3 0.00 ! MET/EMS +SD31B CD32A CD32A CD32A 0.580 1 0.00 ! BUSH +SD31B CD32A CD32A CD32A 0.450 2 0.00 ! BUSH +SD31B CD32A CD32A CD32A 0.200 3 0.00 ! BUSH +SD31B CD32A CD32A CD33A 0.580 1 0.00 ! PRSH +SD31B CD32A CD32A CD33A 0.450 2 0.00 ! PRSH +SD31B CD32A CD32A CD33A 0.200 3 0.00 ! PRSH +SD31B CD32A CD32A HDA2A 0.270 1 0.00 ! PRSH +SD31B CD32A CD32A HDA2A 0.050 2 0.00 ! PRSH +SD31B CD32A CD32A HDA2A 0.120 3 0.00 ! PRSH +CD2O2A CD32A CD32B HDA2A 0.200 3 0.00 ! GLU, c22 +CD30A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +CD31A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +CD32A CD32A CD31C ND3P3A 0.341 1 0.00 ! LYS, NTER, chi1, updated 05/13, jing +CD32A CD32A CD31C ND3P3A 0.622 2 0.00 ! LYS, NTER, chi1 +CD32A CD32A CD31C ND3P3A 1.577 3 0.00 ! LYS, NTER, chi1 +CD31C CD32A CD32A HDA2A 0.190 3 0.00 ! LYS +CD31C CD32B CD32A HDA2A 0.190 3 0.00 ! GLU, from CD31C CD32A CD32A HDA2A +CD31C CD32B CD32C HDA2A 0.190 3 0.00 ! GLUP, from CD31C CD32A CD32A HDA2A +!! +!conflict with 2017 lipids +!original alkane/protein-based parameters +!CD32A CD32A CD32A CD32A 0.073 1 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +!CD32A CD32A CD32A CD32A 0.043 2 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +!CD32A CD32A CD32A CD32A 0.119 3 180.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +!CD32A CD32A CD32A CD32A 0.098 4 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +!CD32A CD32A CD32A CD32A 0.046 5 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +!lipid 2017 parameters: reconcile with above +CD32A CD32A CD32A CD32A 0.005 1 180.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 Hui-2015 +CD32A CD32A CD32A CD32A 0.104 2 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 Hui-2015 +CD32A CD32A CD32A CD32A 0.058 3 180.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 Hui-2015 +CD32A CD32A CD32A CD32A 0.098 4 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 Hui-2015 +CD32A CD32A CD32A CD32A 0.046 5 0.00 ! HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 Hui-2015 +!!! +CD32A CD32A CD32A CD33A 0.093 1 0.00 ! PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD33A 0.143 2 0.00 ! PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD33A 0.055 4 0.00 ! PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD32A CD32A CD32A CD33A 0.102 5 0.00 ! PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, 10/07 +CD31A CD32A CD32A CD33A 0.093 1 0.00 ! from PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, +CD31A CD32A CD32A CD33A 0.143 2 0.00 ! from PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, +CD31A CD32A CD32A CD33A 0.055 4 0.00 ! from PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, +CD31A CD32A CD32A CD33A 0.102 5 0.00 ! from PENT/HEXA/HEPT, hybrid CCSD(T)/cc-pVQZ surf. fit, va, +CD32A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +CD32A CD32A CD32A HDA2C 0.190 3 0.00 ! LYS +CD32E CD32A CD32A CD33A 0.093 1 0.00 ! ethers/DEET +CD32E CD32A CD32A CD33A 0.143 2 0.00 ! ethers/DEET +CD32E CD32A CD32A CD33A 0.055 4 0.00 ! ethers/DEET +CD32E CD32A CD32A CD33A 0.102 5 0.00 ! ethers/DEET +CD32E CD32A CD32A HDA2A 0.190 3 0.00 ! ethers/DEET +CD33A CD32A CD32A CD33A 0.150 1 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A CD33A 0.170 2 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A CD33A 0.114 3 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A CD33A 0.094 4 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A CD33A 0.070 5 0.00 ! BUTA, butane, hybrid CCSD(T)/cc-pVQZ surf. fit, 10/07, va +CD33A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +HDA2A CD32A CD32A HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell +HDA2A CD32B CD32A HDA2A 0.190 3 0.00 ! GLU, from HDA2A CD32A CD32A HDA2A +HDA2A CD32A CD32A HDA2C 0.190 3 0.00 ! LYS +CD31A CD32A CD32C HDA2A 0.190 3 0.00 ! alkane, ester +CD31C CD32B CD32C CD2O3A 0.200 3 0.00 ! GLUP, c22, chi2 +CD31C CD32A CD32C HDA2A 0.190 3 0.00 ! BUTA, butane, 4/98, yin and mackerell ADDED FOR ALAD +CD32A CD32A CD32C HDA2A 0.190 3 0.00 ! alkane, ester +CD33A CD32A CD32C HDA2A 0.190 3 0.00 ! alkane, ester +HDA2A CD32A CD32C CD2O1A 0.200 3 0.00 ! GLN, alkanes +HDA1C CD31C CD32C CD2O1A 0.200 3 0.00 ! PEML by analogy ASN, CTER +HDA2A CD32B CD32C CD2O3A 0.200 3 0.00 ! GLUP, alkane, ester +HDA2A CD32A CD32C HDA2A 0.190 3 0.00 ! alkane, ester +HDA2A CD32B CD32C HDA2A 0.190 3 0.00 ! GLUP, alkane, ester +HDA1C CD31C CD32B HDA2A 0.190 3 0.00 ! PEML by analogy GLU, CTER +HDA1C CD31C CD32C HDA2A 0.190 3 0.00 ! PEML by analogy ASN, CTER +CD32A CD32A CD32E OD30A 0.160 1 180.00 ! MPE, ATM +CD32A CD32A CD32E OD30A 0.390 2 0.00 ! MPE, ATM +CD32A CD32A CD32E HDA2E 0.190 3 0.00 ! ethers/DEET +CD33A CD32A CD32E OD30A 0.160 1 180.00 ! MPE, methylpropylether, 2/12/05, ATM +CD33A CD32A CD32E OD30A 0.390 2 0.00 ! MPE, ATM +CD33A CD32A CD32E HDA2E 0.190 3 0.00 ! ethers/DEET +HDA2A CD32A CD32E OD30A 0.190 3 0.00 ! DEET, diethylether alex +HDA2A CD32A CD32E HDA2E 0.190 3 0.00 ! ethers/DEET +ND3P2A CD32A CD33A HDA3A 0.160 3 0.00 ! NC5, charmm27, ammonium cation +ND3P3A CD32A CD33A HDA3A 0.160 3 0.00 ! NH5, charmm27, ammonium cation +OD30A CD32A CD33A HDA3A 0.160 3 0.00 ! DEET, alex +OD31A CD32A CD32A HDA2C 0.175 3 0.00 ! ETAM, from ethanol +OD31A CD32A CD33A HDA3A 0.175 3 0.00 ! ETOH, ethanol +SD30A CD32A CD33A HDA3A 0.1388 3 0.00 ! EMS +SD31B CD32A CD33A HDA3A 0.175 3 0.00 ! ETSH +CD30A CD32A CD33A HDA3A 0.160 3 0.00 ! PROP, propane, 4/98, yin and mackerell +CD31A CD32A CD33A HDA3A 0.160 3 0.00 ! PROP, propane, 4/98, yin and mackerell +CD31C CD32A CD33A HDA3A 0.160 3 0.00 ! PROP, propane, 4/98, yin and mackerell ADDED FOR ALAD +CD32A CD32A CD33A HDA3A 0.140 3 0.00 ! BUTA, butane, 10/07, va +CD326A CD316A CD33A HDA3A 0.140 3 0.00 ! CHXM, from BUTA, butane, 10/07, va, cmb 12/09 +CD32C CD32A CD33A HDA3A 0.160 3 0.00 ! MBU, alkane, ester +CD32E CD32A CD33A HDA3A 0.140 3 0.00 ! ethers/DEET +CD33A CD32A CD33A HDA3A 0.185 3 0.00 ! PROP, propane, 10/07, va +HDA2A CD32A CD33A HDA3A 0.145 3 0.00 ! PROP, propane, butane, 10/07, va +HDA2C CD32A CD33A HDA3A 0.160 3 0.00 ! NC5, charmm27, ammonium cation +OD30C CD32C CD33A HDA3A 0.160 3 0.00 ! EAS, charmm27 +HDA2A CD32C CD33A HDA3A 0.160 3 0.00 ! alkane, ester +OD30A CD32E CD32E OD30A 0.3681 1 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 1.2036 2 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 0.1171 3 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 0.1612 4 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 0.0340 5 0.00 ! DMOE, viv +OD30A CD32E CD32E OD30A 0.0225 6 0.00 ! DMOE, viv +OD30A CD32E CD32E HDA2E 0.190 3 0.00 ! DEET, diethylether alex +HDA2E CD32E CD32E HDA2E 0.190 3 0.00 ! ethers/DEET +OD30A CD32E CD33A HDA3A 0.160 3 0.00 ! DEET, alex +HDA2E CD32E CD33A HDA3A 0.145 3 0.00 ! ethers/DEET +HDA3A CD33A CD33A HDA3A 0.144 3 0.00 ! ETHA, ethane, 10/07, va +!!! FOR TYR-NTER +HDA1C CD31A CD32A CD2R6A 0.040 3 0.00 ! PHE, c22 +CD2R6A CD32A CD31A CD2O2A 0.040 3 0.00 ! TO ALLOW NTER-TYR-CTER +!!! FOR PHE-CNEU +CD2R6A CD32A CD31C CD2O3A 0.040 3 0.00 ! PHE, c22, chi1 +! Protein chi1/2 fitting +! Variable cutoff based on QM and weighted for alphaR and EXT +! Shared terms were fitted simultaneously +! Manually adjust to reproduce chi1, chi2 distribution from pdb survey data, jing +! Group-fitted side-chain for lys/arg/met +CD31C CD32A CD32A CD32A 0.098 1 0.00 ! RMSE = 2.63237 +CD31C CD32A CD32A CD32A 0.206 2 180.00 ! RMSE = 2.63237 0.236 0.236 2 +CD31C CD32A CD32A CD32A 0.319 3 180.00 ! RMSE = 2.63237 +ND2A2 CD31C CD32A CD32A 0.488 1 180.00 ! RMSE = 2.63237 1.071 1.071 1 +ND2A2 CD31C CD32A CD32A 1.206 2 0.00 ! RMSE = 2.63237 0.020 0.020 2 +ND2A2 CD31C CD32A CD32A 1.065 3 0.00 ! RMSE = 2.63237 1.065 1.065 3 +CD2O1A CD31C CD32A CD32A 1.398 1 180.00 ! RMSE = 2.63237 1.398 1.398 1 +CD2O1A CD31C CD32A CD32A 0.201 2 180.00 ! RMSE = 2.63237 0.201 0.201 2 +CD2O1A CD31C CD32A CD32A 0.856 3 180.00 ! RMSE = 2.63237 0.856 0.856 3 +CD31C CD32A CD32A SD30A 0.307 1 180.00 ! RMSE = 2.63237 0.307 0.307 1 +CD31C CD32A CD32A SD30A 0.212 2 180.00 ! RMSE = 2.63237 0.212 0.212 2 +CD31C CD32A CD32A SD30A 0.381 3 180.00 ! RMSE = 2.63237 0.381 0.381 3 +! Group-fitted side-chain for asn +ND2A1 CD2O1A CD32C CD31C 2.713 1 180.00 ! RMSE = 2.49354 +ND2A1 CD2O1A CD32C CD31C 1.850 2 180.00 ! RMSE = 2.49354 +ND2A1 CD2O1A CD32C CD31C 0.228 3 0.00 ! RMSE = 2.49354 +OD2C1A CD2O1A CD32C CD31C 2.933 1 180.00 ! RMSE = 2.49354 +OD2C1A CD2O1A CD32C CD31C 0.767 2 0.00 ! RMSE = 2.49354 +OD2C1A CD2O1A CD32C CD31C 0.081 3 180.00 ! RMSE = 2.49354 +CD2O1A CD31C CD32C CD2O1A 1.592 1 180.00 ! RMSE = 2.49354 +CD2O1A CD31C CD32C CD2O1A 0.232 2 180.00 ! RMSE = 2.49354 +CD2O1A CD31C CD32C CD2O1A 1.093 3 180.00 ! RMSE = 2.49354 +ND2A2 CD31C CD32C CD2O1A 0.394 1 0.00 ! RMSE = 2.49354 +ND2A2 CD31C CD32C CD2O1A 0.630 2 180.00 ! RMSE = 2.49354 +ND2A2 CD31C CD32C CD2O1A 0.767 3 0.00 ! RMSE = 2.49354 +! Group-fitted side-chain for asp (cb 0.75) +OD2C2A CD2O2A CD32A CD31C 0.726 1 180.00 ! RMSE = 3.34692 +OD2C2A CD2O2A CD32A CD31C 1.073 2 180.00 ! RMSE = 3.34692 +OD2C2A CD2O2A CD32A CD31C 0.527 3 0.00 ! RMSE = 3.34692 +CD2O1A CD31C CD32A CD2O2A 1.303 1 180.00 ! RMSE = 3.34692 +CD2O1A CD31C CD32A CD2O2A 1.109 2 180.00 ! RMSE = 3.34692 +CD2O1A CD31C CD32A CD2O2A 1.163 3 180.00 ! RMSE = 3.34692 +ND2A2 CD31C CD32A CD2O2A 1.974 1 0.00 ! RMSE = 3.34692 0.544 +ND2A2 CD31C CD32A CD2O2A 1.407 2 0.00 ! RMSE = 3.34692 1.256 +ND2A2 CD31C CD32A CD2O2A 0.474 3 0.00 ! RMSE = 3.34692 0.774 +! Fitted cys side-chain +CD31C CD32A SD31B HDP1A 0.245 1 180.00 ! RMSE = 1.72955 +CD31C CD32A SD31B HDP1A 0.693 2 0.00 ! RMSE = 1.72955 +CD31C CD32A SD31B HDP1A 0.470 3 0.00 ! RMSE = 1.72955 +CD2O1A CD31C CD32A SD31B 0.551 1 0.00 ! RMSE = 1.72955 +CD2O1A CD31C CD32A SD31B 0.271 2 180.00 ! RMSE = 1.72955 +CD2O1A CD31C CD32A SD31B 1.071 3 180.00 ! RMSE = 1.72955 +ND2A2 CD31C CD32A SD31B 0.159 1 0.00 ! RMSE = 1.72955 +ND2A2 CD31C CD32A SD31B 0.298 2 180.00 ! RMSE = 1.72955 +ND2A2 CD31C CD32A SD31B 1.441 3 0.00 ! RMSE = 1.72955 +! Group-fitted side-chain for gln +CD31C CD32A CD32C CD2O1A 0.385 1 180.00 ! RMSE = 1.99947 +CD31C CD32A CD32C CD2O1A 0.376 2 180.00 ! RMSE = 1.99947 +CD31C CD32A CD32C CD2O1A 0.422 3 180.00 ! RMSE = 1.99947 +CD2O1A CD31C CD32A CD32C 1.265 1 0.00 ! RMSE = 1.99947 +CD2O1A CD31C CD32A CD32C 0.052 2 180.00 ! RMSE = 1.99947 +CD2O1A CD31C CD32A CD32C 0.609 3 180.00 ! RMSE = 1.99947 +ND2A2 CD31C CD32A CD32C 0.998 1 180.00 ! RMSE = 1.99947 +ND2A2 CD31C CD32A CD32C 0.027 2 0.00 ! RMSE = 1.99947 +ND2A2 CD31C CD32A CD32C 0.742 3 0.00 ! RMSE = 1.99947 +! Group-fitted side-chain for glu (cb.cg) +CD2O2A CD32A CD32B CD31C 0.760 1 180.00 ! RMSE = 4.33515 +CD2O2A CD32A CD32B CD31C 3.370 2 180.00 ! RMSE = 4.23825 0.670 2 0.00 +CD2O2A CD32A CD32B CD31C 0.808 3 180.00 ! RMSE = 4.23825 0.808 3 180.00 +CD2O1A CD31C CD32B CD32A 1.061 1 0.00 ! RMSE = 4.23825 1.961 1 0.00 +CD2O1A CD31C CD32B CD32A 0.486 2 180.00 ! RMSE = 4.23825 0.486 2 180.00 +CD2O1A CD31C CD32B CD32A 0.172 3 0.00 ! RMSE = 4.23825 0.172 3 0.00 +CD2O1A CD31C CD32B CD32C 1.061 1 0.00 ! RMSE = 4.33515 ! Terminal patc 1.961 1 0.00 +CD2O1A CD31C CD32B CD32C 0.486 2 180.00 ! RMSE = 4.33515 0.486 2 180.00 +CD2O1A CD31C CD32B CD32C 0.172 3 0.00 ! RMSE = 4.33515 0.172 3 0.00 +ND2A2 CD31C CD32B CD32A 2.331 1 180.00 ! RMSE = 4.23825 0.331 1 180.00 +ND2A2 CD31C CD32B CD32A 0.344 2 0.00 ! RMSE = 4.23825 0.344 2 0.00 +ND2A2 CD31C CD32B CD32A 0.155 3 180.00 ! RMSE = 4.23825 0.155 3 180.00 +ND2A2 CD31C CD32B CD32C 2.331 1 180.00 ! RMSE = 4.33515 GLUP 0.331 1 180.00 +ND2A2 CD31C CD32B CD32C 0.344 2 0.00 ! RMSE = 4.33515 GLUP 0.344 2 0.00 +ND2A2 CD31C CD32B CD32C 0.155 3 180.00 ! RMSE = 4.33515 GLUP 0.155 3 180.00 +! Group-fitted side-chain for hsd/hse +CD2R5A CD2R5A CD32A CD31C 0.313 1 180.00 ! RMSE = 1.79492 +CD2R5A CD2R5A CD32A CD31C 0.503 2 0.00 ! RMSE = 1.79492 +CD2R5A CD2R5A CD32A CD31C 0.180 3 0.00 ! RMSE = 1.79492 +ND2R5A CD2R5A CD32A CD31C 0.405 1 180.00 ! RMSE = 1.79492 +ND2R5A CD2R5A CD32A CD31C 0.258 2 0.00 ! RMSE = 1.79492 +ND2R5A CD2R5A CD32A CD31C 0.800 3 0.00 ! RMSE = 1.79492 +ND2R5B CD2R5A CD32A CD31C 0.001 1 0.00 ! RMSE = 1.79492 +ND2R5B CD2R5A CD32A CD31C 0.057 2 180.00 ! RMSE = 1.79492 +ND2R5B CD2R5A CD32A CD31C 0.593 3 0.00 ! RMSE = 1.79492 +CD2O1A CD31C CD32A CD2R5A 0.282 1 180.00 ! RMSE = 1.79492 0.082 ! +CD2O1A CD31C CD32A CD2R5A 0.208 2 180.00 ! RMSE = 1.79492 0.408 ! +CD2O1A CD31C CD32A CD2R5A 1.035 3 180.00 ! RMSE = 1.79492 1.035 +ND2A2 CD31C CD32A CD2R5A 0.700 1 180.00 ! RMSE = 1.79492 0.500 ! +ND2A2 CD31C CD32A CD2R5A 0.466 2 180.00 ! RMSE = 1.79492 0.666 ! +ND2A2 CD31C CD32A CD2R5A 0.984 3 0.00 ! RMSE = 1.79492 0.984 +! Group-fitted side-chain for hsp +CD2R5D CD2R5D CD32A CD31C 0.467 1 180.00 ! RMSE = 2.44077 +CD2R5D CD2R5D CD32A CD31C 1.227 2 180.00 ! RMSE = 2.44077 +CD2R5D CD2R5D CD32A CD31C 0.748 3 180.00 ! RMSE = 2.44077 +ND2R5C CD2R5D CD32A CD31C 1.474 1 180.00 ! RMSE = 2.44077 +ND2R5C CD2R5D CD32A CD31C 1.764 2 0.00 ! RMSE = 2.44077 +ND2R5C CD2R5D CD32A CD31C 0.574 3 180.00 ! RMSE = 2.44077 +CD2O1A CD31C CD32A CD2R5D 0.953 1 180.00 ! RMSE = 2.44077 +CD2O1A CD31C CD32A CD2R5D 0.374 2 0.00 ! RMSE = 2.44077 +CD2O1A CD31C CD32A CD2R5D 1.343 3 180.00 ! RMSE = 2.44077 +ND2A2 CD31C CD32A CD2R5D 2.020 1 180.00 ! RMSE = 2.44077 +ND2A2 CD31C CD32A CD2R5D 0.204 2 180.00 ! RMSE = 2.44077 +ND2A2 CD31C CD32A CD2R5D 1.559 3 0.00 ! RMSE = 2.44077 +! Group-fitted side-chain for ile/val +CD31C CD31A CD32A CD33A 0.023 1 180.00 ! RMSE = 1.86101 0.023 +CD31C CD31A CD32A CD33A 1.588 2 180.00 ! RMSE = 1.86101 0.088 +CD31C CD31A CD32A CD33A 0.013 3 0.00 ! RMSE = 1.86101 0.013 +CD32A CD31A CD31C CD2O1A 0.378 1 0.00 ! RMSE = 1.86101 0.378 +CD32A CD31A CD31C CD2O1A 0.259 2 180.00 ! RMSE = 1.86101 +CD32A CD31A CD31C CD2O1A 0.109 3 180.00 ! RMSE = 1.86101 0.109 +CD32A CD31A CD31C ND2A2 0.796 1 0.00 ! RMSE = 1.86101 0.796 +CD32A CD31A CD31C ND2A2 1.622 2 0.00 ! RMSE = 1.86101 0.122 +CD32A CD31A CD31C ND2A2 0.365 3 0.00 ! RMSE = 1.86101 0.365 +! Fitted leu side-chain +CD33A CD31A CD32A CD31C 0.202 1 180.00 ! RMSE = 1.84353 +CD33A CD31A CD32A CD31C 0.190 2 180.00 ! RMSE = 1.84353 +CD33A CD31A CD32A CD31C 0.058 3 0.00 ! RMSE = 1.84353 +CD2O1A CD31C CD32A CD31A 0.737 1 180.00 ! RMSE = 1.84353 +CD2O1A CD31C CD32A CD31A 0.062 2 0.00 ! RMSE = 1.84353 +CD2O1A CD31C CD32A CD31A 0.665 3 180.00 ! RMSE = 1.84353 +ND2A2 CD31C CD32A CD31A 0.116 1 180.00 ! RMSE = 1.84353 +ND2A2 CD31C CD32A CD31A 0.258 2 0.00 ! RMSE = 1.84353 +ND2A2 CD31C CD32A CD31A 0.693 3 0.00 ! RMSE = 1.84353 +! Group-fitted side-chain for phe/tyr +CD2R6A CD2R6A CD32A CD31C 0.275 1 180.00 ! RMSE = 1.50422 0.275 1 180.00 +CD2R6A CD2R6A CD32A CD31C 0.171 2 0.00 ! RMSE = 1.50422 +CD2R6A CD2R6A CD32A CD31C 0.082 3 0.00 ! RMSE = 1.50422 0.082 3 0.00 +CD2O1A CD31C CD32A CD2R6A 0.665 1 180.00 ! RMSE = 1.50422 0.665 1 180.00 +CD2O1A CD31C CD32A CD2R6A 0.498 2 180.00 ! RMSE = 1.50422 0.498 2 180.00 +CD2O1A CD31C CD32A CD2R6A 0.832 3 180.00 ! RMSE = 1.50422 0.832 3 180.00 +ND2A2 CD31C CD32A CD2R6A 0.588 1 180.00 ! RMSE = 1.50422 0.588 1 180.00 +ND2A2 CD31C CD32A CD2R6A 0.830 2 180.00 ! RMSE = 1.50422 0.830 2 180.00 +ND2A2 CD31C CD32A CD2R6A 0.782 3 0.00 ! RMSE = 1.50422 0.782 3 0.00 +! Fitted ser side-chain +CD31C CD32A OD31A HDP1A 0.068 1 0.00 ! RMSE = 1.73077 +CD31C CD32A OD31A HDP1A 0.486 2 0.00 ! RMSE = 1.73077 +CD31C CD32A OD31A HDP1A 0.316 3 0.00 ! RMSE = 1.73077 +CD2O1A CD31C CD32A OD31A 1.006 1 180.00 ! RMSE = 1.73077 +CD2O1A CD31C CD32A OD31A 0.658 2 180.00 ! RMSE = 1.73077 +CD2O1A CD31C CD32A OD31A 0.878 3 180.00 ! RMSE = 1.73077 +ND2A2 CD31C CD32A OD31A 0.350 1 180.00 ! RMSE = 1.73077 +ND2A2 CD31C CD32A OD31A 0.833 2 180.00 ! RMSE = 1.73077 +ND2A2 CD31C CD32A OD31A 1.125 3 0.00 ! RMSE = 1.73077 +! Group-fitted side-chain for thr/val +CD31C CD31A OD31A HDP1A 0.528 1 0.00 ! RMSE = 2.11193 +CD31C CD31A OD31A HDP1A 0.296 2 0.00 ! RMSE = 2.11193 +CD31C CD31A OD31A HDP1A 0.268 3 0.00 ! RMSE = 2.11193 +OD31A CD31A CD31C CD2O1A 1.466 1 0.00 ! RMSE = 2.11193 +OD31A CD31A CD31C CD2O1A 0.365 2 180.00 ! RMSE = 2.11193 +OD31A CD31A CD31C CD2O1A 0.430 3 180.00 ! RMSE = 2.11193 +OD31A CD31A CD31C ND2A2 0.290 1 0.00 ! RMSE = 2.11193 +OD31A CD31A CD31C ND2A2 1.361 2 0.00 ! +OD31A CD31A CD31C ND2A2 0.792 3 0.00 ! RMSE = 2.11193 +! Fitted trp side-chain +CD2R5A CD2R5C CD32A CD31C 0.397 1 180.00 ! RMSE = 1.37514 +CD2R5A CD2R5C CD32A CD31C 0.797 2 0.00 ! RMSE = 1.37514 0.297 +CD2R5A CD2R5C CD32A CD31C 0.387 3 180.00 ! RMSE = 1.37514 0.387 +CD2R6D CD2R5C CD32A CD31C 0.358 1 180.00 ! RMSE = 1.37514 0.358 ! +CD2R6D CD2R5C CD32A CD31C 0.651 2 0.00 ! RMSE = 1.37514 0.151 +CD2R6D CD2R5C CD32A CD31C 0.191 3 0.00 ! RMSE = 1.37514 +CD2O1A CD31C CD32A CD2R5C 0.103 1 180.00 ! RMSE = 1.37514 +CD2O1A CD31C CD32A CD2R5C 0.347 2 180.00 ! RMSE = 1.37514 +CD2O1A CD31C CD32A CD2R5C 0.968 3 180.00 ! RMSE = 1.37514 +ND2A2 CD31C CD32A CD2R5C 0.879 1 180.00 ! RMSE = 1.37514 +ND2A2 CD31C CD32A CD2R5C 0.548 2 180.00 ! RMSE = 1.37514 +ND2A2 CD31C CD32A CD2R5C 0.974 3 0.00 ! RMSE = 1.37514 +! Fitted val side-chain +CD33A CD31A CD31C CD2O1A 0.273 1 0.00 ! RMSE = 1.11304 +CD33A CD31A CD31C CD2O1A 0.626 2 180.00 ! RMSE = 1.11304 0.126 2 180.00 +CD33A CD31A CD31C CD2O1A 0.393 3 180.00 ! RMSE = 1.11304 0.393 3 180.00 +CD33A CD31A CD31C ND2A2 0.422 1 0.00 ! RMSE = 1.11304 0.422 1 0.00 +CD33A CD31A CD31C ND2A2 0.588 2 0.00 ! RMSE = 1.11304 0.088 2 0.00 +CD33A CD31A CD31C ND2A2 0.736 3 0.00 ! RMSE = 1.11304 +!! end + +CD2O1A CD32C CD31C ND3P3A 1.432 1 0.00 ! PEML by analogy ASN NTER +CD2O1A CD32C CD31C ND3P3A 1.356 2 180.00 ! PEML by analogy ASN NTER +CD2O1A CD32C CD31C ND3P3A 0.038 3 180.00 ! PEML by analogy ASN NTER +ND3P3A CD31C CD32A SD31B 0.562 1 180.00 ! PEML by analogy CYS NTER +ND3P3A CD31C CD32A SD31B 0.192 2 180.00 ! PEML by analogy CYS NTER +ND3P3A CD31C CD32A SD31B 1.696 3 0.00 ! PEML by analogy CYS NTER +CD2O2A CD31C CD32A OD31A 0.834 1 0.00 ! PEML by analogy SER +CD2O2A CD31C CD32A OD31A 0.664 2 0.00 ! PEML by analogy SER +CD2O2A CD31C CD32A OD31A 1.064 3 180.00 ! PEML by analogy SER +CD2O3A CD31C CD32A OD31A 0.834 1 0.00 ! PEML by analogy SER +CD2O3A CD31C CD32A OD31A 0.664 2 0.00 ! PEML by analogy SER +CD2O3A CD31C CD32A OD31A 1.064 3 180.00 ! PEML by analogy SER +CD2O3A CD31C CD31A OD31A 0.834 1 0.00 ! PEML by analogy THR +CD2O3A CD31C CD31A OD31A 0.664 2 0.00 ! PEML by analogy THR +CD2O3A CD31C CD31A OD31A 1.064 3 180.00 ! PEML by analogy THR +CD2O2A CD31C CD32A SD30B 0.834 1 0.00 ! alex by analogy CYS +CD2O2A CD31C CD32A SD30B 0.664 2 0.00 ! alex by analogy CYS +CD2O2A CD31C CD32A SD30B 1.064 3 180.00 ! alex by analogy CYS +! FROM ANALOGY ABOVE - PEML: VERIFY ! +ND3A3 CD2O1A CD31C CD32B 0.200 3 0.00 ! PRO +HDA1C CD31C CD32A OD31A 0.270 1 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD32A OD31A 0.050 2 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD32A OD31A 0.120 3 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD31A OD31A 0.270 1 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD31A OD31A 0.050 2 0.00 ! SER/PRO1, 1-propanol +HDA1C CD31C CD31A OD31A 0.120 3 0.00 ! SER/PRO1, 1-propanol +ND3P3A CD31C CD32A OD31A 0.500 2 0.00 ! FROM ANALOGY ABOVE - PEML: VERIFY !!!!!!!!!!!!!!!!!!!!!!!!! +ND3P3A CD31C CD32A OD31A 0.500 3 0.00 ! Discovered when doing protein tests using Xiao's proteins +ND3P3A CD31C CD31A OD31A 0.500 2 0.00 ! PEML: Appeared on Crambin xtal simulations: THR-NTER +ND3P3A CD31C CD31A OD31A 0.500 3 0.00 ! PEML: Appeared on Crambin xtal simulations: THR-NTER +CD31A CD31C CD2O1A ND2A1 0.000 1 0.00 ! PRES CT2, guess +CD32A CD31C CD2O1A ND2A1 0.000 1 0.00 ! PRES CT2, guess +CD32B CD31C CD2O1A ND2A1 0.000 1 0.00 ! PRES CT2, guess +! CT1 +! +CD33C OD30C CD2O3A OD2C3A 0.229 1 0.00 ! MAS, C1-OM-C-O +CD33C OD30C CD2O3A OD2C3A 3.567 2 180.00 ! MAS +CD33C OD30C CD2O3A OD2C3A 0.049 3 180.00 ! MAS +CD33C OD30C CD2O3A OD2C3A 0.040 6 180.00 ! MAS +!!!!!!!!!!!!!!alkenes 2022 parameters !!!!!!!!!!!!!!!!!!!!!!!!!!!!! +HD2C1B CD2C1B CD2C1B HD2C1B 5.7300 2 180.00 ! ETHE ; pc 06/2022 +CD33A CD2C1A CD2C1B HD2C1B 4.8900 2 180.00 ! PRPE +HD2C1A CD2C1A CD2C1B HD2C1B 5.0300 2 180.00 ! PRPE, BTE1, PTE1, HXE1 +CD2C1B CD2C1A CD33A HDA3A 0.3447 3 180.00 ! PRPE +CD2C1A CD32A CD33A HDA3A 0.156 3 0.000 !BTE1, 2BTE, PTE1, 2PTE, 2HEX, HXE1 ; pc 06/2022 +CD32A CD2C1A CD2C1B HD2C1B 4.8900 2 180.00 !BTE1, HXE1, PTE1 ; pc 06/2022 +HD2C1A CD2C1A CD32A CD33A 0.1520 2 180.00 ! BTE1; pc 06/2022 +HD2C1A CD2C1A CD32A CD33A 0.8592 3 0.00 ! BTE1; pc 06/2022 +CD2C1B CD2C1A CD32A CD33A 1.0160 1 180.00 ! BTE1; pc 06/2022 +CD2C1B CD2C1A CD32A CD33A 0.3005 2 180.00 ! BTE1; pc 06/2022 +CD2C1B CD2C1A CD32A CD33A 0.4227 3 180.00 ! BTE1; pc 06/2022 +CD2C1B CD2C1A CD32A CD33A 0.1587 4 180.00 ! BTE1; pc 06/2022 +CD2C1B CD2C1A CD32A HDA2A 0.0156 1 0.00 ! BTE1, HTE1, HXE1, PTE1 pc 06/2022 +CD2C1B CD2C1A CD32A HDA2A 0.0121 4 0.00 ! BTE1, HTE1, HXE1, PTE1 pc 06/2022 +CD33A CD2C1A CD2C1A CD33A 0.7120 1 180.00 ! 2BTE ; pc 06/2022 +CD33A CD2C1A CD2C1A CD33A 5.5000 2 180.00 ! 2BTE ; pc 06/2022 +CD33A CD2C1A CD2C1A CD33A 0.4200 3 0.00 ! 2BTE ; pc 06/2022 +CD33A CD2C1A CD2C1A HD2C1A 4.0900 2 180.00 ! 2BTE ; pc 06/2022 +HD2C1A CD2C1A CD2C1A HD2C1A 5.7300 2 180.00 ! 2BTE ; pc 06/2022 +CD2C1A CD32A CD32A CD32A 0.061 1 180.00 ! 2PTE ; pc 06/2022 +CD2C1A CD32A CD32A CD32A 0.149 2 0.00 ! 2PTE ; pc 06/2022 +CD2C1A CD32A CD32A CD32A 0.075 3 0.00 ! 2PTE ; pc 06/2022 +CD32A CD32A CD2C1A HD2C1A 0.000 2 0.00 ! PTE1, HXE1, 2HEX ; pc 06/2022 +CD2C1A CD32A CD32A HDA2A 0.1560 3 0.00 ! PTE1, HXE1, 2HEX ; pc 06/2022 +CD2C1A CD2C1A CD32A CD33A 1.2130 1 180.00 ! 2PTE; 3HEX; pc 10/2022 +CD2C1A CD2C1A CD32A CD33A 0.1280 2 180.00 ! 2PTE; 3HEX; pc 10/2022 +CD2C1A CD2C1A CD32A CD33A 0.0655 3 0.00 ! 2PTE; 3HEX; pc 10/2022 +CD2C1A CD2C1A CD32A CD33A 0.1919 4 180.00 ! 2PTE; 3HEX; pc 10/2022 +CD2C1A CD2C1A CD32A HDA2A 0.0374 1 0.00 ! 2PTE; 2HEX; 3HEX; pc 10/2022 +CD2C1A CD2C1A CD32A HDA2A 0.0021 2 0.00 ! 2PTE; 2HEX; 3HEX; pc 10/2022 +CD2C1A CD2C1A CD32A HDA2A 0.2439 3 180.00 ! 2PTE; 2HEX; 3HEX; pc 10/2022 +CD2C1A CD2C1A CD32A HDA2A 0.0750 4 180.00 ! 2PTE; 2HEX; 3HEX; pc 10/2022 +CD2C1B CD2C1A CD32A CD32A 0.9197 1 180.00 ! PTE1;HXE1;pc 06/2022 +CD2C1B CD2C1A CD32A CD32A 0.3206 2 180.00 ! PTE1;HXE1;pc 06/2022 +CD2C1B CD2C1A CD32A CD32A 1.2209 3 180.00 ! PTE1;HXE1;pc 06/2022 +CD2C1B CD2C1A CD32A CD32A 0.1867 4 180.00 ! PTE1;HXE1;pc 06/2022 +CD2C1A CD32A CD32A CD33A 0.7555 1 180.00 ! 2HEX ;pc 10/2022 +CD2C1A CD32A CD32A CD33A 0.2406 2 180.00 ! 2HEX ;pc 10/2022 +CD2C1A CD32A CD32A CD33A 0.1317 3 180.00 ! 2HEX ;pc 10/2022 +CD32A CD2C1A CD2C1A CD33A 0.5065 1 180.00 ! 2PTE ; 2HEX; pc 10/2022 +CD32A CD2C1A CD2C1A CD33A 4.2207 2 180.00 ! 2PTE ; 2HEX; pc 10/2022 +CD32A CD2C1A CD2C1A CD33A 0.3327 3 0.00 ! 2PTE ; 2HEX; pc 10/2022 +CD32A CD2C1A CD2C1A CD33A 0.4226 4 180.00 ! 2PTE ; 2HEX; pc 10/2022 +CD2C1A CD2C1A CD32A CD32A 1.2276 1 180.00 ! 2HEX ; pc 10/2022 +CD2C1A CD2C1A CD32A CD32A 0.1828 2 180.00 ! 2HEX ; pc 10/2022 +CD2C1A CD2C1A CD32A CD32A 0.7410 3 180.00 ! 2HEX ; pc 10/2022 +CD2C1A CD2C1A CD32A CD32A 0.1882 4 180.00 ! 2HEX ; pc 10/2022 +HD2C1A CD2C1A CD32A HDA2A 0.000 2 0.00 ! BTE1, 2BTE, PTE1, 2PTE, 2HEX, HXE1 ; pc 06/2022 +CD32A CD2C1A CD2C1A HD2C1A 5.5000 2 180.00 ! Hui-v9 +CD2C1A CD2C1A CD33A HDA3A 0.3802 3 180.00 ! 2BTE, 2PTE , 2HEX; pc 06/2022 +HD2C1A CD2C1A CD33A HDA3A 0.4912 2 0.00 ! 2BTE, 2PTE , 2HEX pc 06/2022 +CD32A CD2C1A CD2C1A CD32A 0.6793 1 180.00 ! 3HEX; pc 06/2022 +CD32A CD2C1A CD2C1A CD32A 6.7271 2 180.00 ! 3HEX; pc 06/2022 +CD32A CD2C1A CD2C1A CD32A 0.4002 3 0.00 ! 3HEX; pc 06/2022 +CD32A CD2C1A CD2C1A CD32A 1.2709 4 0.00 ! 3HEX; pc 06/2022 +HD2C1A CD2C1A CD326A CD326A 0.0136 1 0.00 ! CHXE; pc 06/2022 +HD2C1A CD2C1A CD326A CD326A 0.3828 2 0.00 ! CHXE; pc 06/2022 +HD2C1A CD2C1A CD326A CD326A 0.9067 3 180.00 ! CHXE; pc 06/2022 +HD2C1A CD2C1A CD326A CD326A 1.1955 4 180.00 ! CHXE; pc 06/2022 +CD2C1A CD2C1A CD326A CD326A 5.4228 1 180.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD2C1A CD326A CD326A 1.9564 2 180.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD2C1A CD326A CD326A 1.8091 3 180.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD2C1A CD326A HDA2A 0.3989 3 0.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD326A CD326A CD326A 4.6566 1 0.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD326A CD326A CD326A 3.4204 2 0.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD326A CD326A CD326A 0.4643 3 0.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD326A CD326A CD326A 3.0193 4 180.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD326A CD326A CD326A 0.8642 5 0.00 ! CHXE cyclic alkenes;pc 07/2022;n=5 extremely importat for overall geometry;pc 07/2022 +CD326A CD2C1A CD2C1A CD326A 0.0599 1 0.00 ! CHXE cyclic alkenes;pc 07/2022 +CD326A CD2C1A CD2C1A CD326A 0.0243 2 180.00 ! CHXE cyclic alkenes;pc 07/2022 +CD326A CD2C1A CD2C1A CD326A 0.1405 3 180.00 ! CHXE cyclic alkenes;pc 07/2022 +CD326A CD2C1A CD2C1A CD326A 0.2438 4 180.00 ! CHXE cyclic alkenes;pc 07/2022 +CD326A CD2C1A CD2C1A CD326A 0.2478 5 180.00 ! CHXE cyclic alkenes;pc 07/2022; n=5 extremely importnt for overall geometry;pc 07/2022 +HD2C1A CD2C1A CD326A HDA2A 0.1672 2 180.00 ! CHXE cyclic alkenes;pc 07/2022 +HD2C1A CD2C1A CD326A HDA2A 0.4584 3 0.00 ! CHXE cyclic alkenes;pc 07/2022 +CD2C1A CD326A CD326A HDA2A 0.1900 3 0.00 ! CHXE; pc 06/2022 +CD326A CD2C1A CD2C1A HD2C1A 5.5000 2 180.00 ! CHXE; pc 06/2022 +! 2022 alkene update from Payal, end + +!carbonyls +CD33A CD31C CD33A HDA3A 0.150 3 0.00 ! IBUT, isobutane, 10/07, va +CD2O1C CD31C CD33A HDA3A 0.200 3 0.00 ! CNEU +HDP1C CD2O1C CD31C HDA1A 0.200 3 0.00 ! +OD2C1C CD2O1C CD31C HDA1A 0.085 3 0.00 ! +CD33C CD2O1D CD33C HDA3A 0.200 3 0.00 ! acetone +CD32C CD2O1D CD33C HDA3A 0.200 3 0.00 ! +CD32C CD2O1D CD32C HDA2A 0.200 3 0.00 ! 3-pentanone +CD33C CD2O1D CD32C HDA2A 0.200 3 0.00 ! +OD2C1D CD2O1D CD33C HDA3A 0.085 3 0.00 ! acetone, ; +OD2C1D CD2O1D CD32C HDA2A 0.085 3 0.00 ! +CD2O1D CD32C CD33A HDA3A 0.120 3 180.00 ! 3-pentanone 0.120, +CD2O1D CD32C CD32A HDA2A 0.200 3 180.00 !2-pentanone +HDP1C CD2O1C CD32C HDA2A 0.200 3 0.00 ! ethanal +HDP1C CD2O1C CD33C HDA3A 0.200 3 0.00 ! +CD2O1C CD32C CD33A HDA3A 0.120 3 180.00 ! +CD33A CD32A CD32C CD2O1C 0.5501 1 0.00 ! +CD33A CD32A CD32C CD2O1C 0.9806 2 0.00 ! +CD33A CD32A CD32C CD2O1C 0.3445 3 0.00 ! +CD2O1C CD32C CD32A HDA2A 0.200 3 180.00 ! +OD2C1C CD2O1C CD33C HDA3A 0.015 3 0.00 ! +OD2C1C CD2O1C CD32C HDA2A 0.015 3 0.00 ! +CD2O1C CD31G CD31G HDA1A 0.5750 1 0.00 ! +CD2O1C CD31G CD31G HDA1A 0.4780 2 0.00 ! +CD2O1C CD31G CD31G HDA1A 0.2480 3 0.00 ! +CD2O1C CD31G CD31G OD31E 0.3100 1 0.00 ! +CD2O1C CD31G CD31G OD31E 0.1370 2 0.00 ! +CD2O1C CD31G CD31G OD31E 0.1130 3 0.00 ! +CD2O1C CD31G CD31G CD31G 1.5480 1 180.00 ! +CD2O1C CD31G CD31G CD31G 0.3290 2 180.00 ! +CD2O1C CD31G CD31G CD31G 0.0960 3 180.00 ! +CD2O1D CD31G CD31G CD31G 1.5480 1 180.00 ! +CD2O1D CD31G CD31G CD31G 0.3290 2 180.00 ! +CD2O1D CD31G CD31G CD31G 0.0960 3 180.00 ! +CD2O1D CD31G CD31G HDA1A 0.200 3 0.00 ! +CD2O1D CD31G CD31G OD31E 0.3100 1 0.00 ! +CD2O1D CD31G CD31G OD31E 0.1370 2 0.00 ! +CD2O1D CD31G CD31G OD31E 0.1130 3 0.00 ! +CD2O1D CD32F OD31E HDP1A 0.5750 1 0.00 ! +CD2O1D CD32F OD31E HDP1A 0.4780 2 0.00 ! +CD2O1D CD32F OD31E HDP1A 0.2480 3 0.00 ! +CD2O1D CD31G OD31E HDP1A 0.5750 1 0.00 ! +CD2O1D CD31G OD31E HDP1A 0.4780 2 0.00 ! +CD2O1D CD31G OD31E HDP1A 0.2480 3 0.00 ! +!bton +CD33C CD2O1D CD32C CD33A 0.3865 1 0.00 ! +CD33C CD2O1D CD32C CD33A 0.1195 2 180.00 ! +CD33C CD2O1D CD32C CD33A 0.0911 3 0.00 ! +CD33C CD2O1D CD32C CD33A 0.0307 6 0.00 ! +OD2C1D CD2O1D CD32C CD33A 0.3890 1 180.00 ! +OD2C1D CD2O1D CD32C CD33A 0.2715 2 180.00 ! +OD2C1D CD2O1D CD32C CD33A 0.0825 3 180.00 ! +OD2C1D CD2O1D CD32C CD33A 0.0164 6 0.00 ! +!pald +OD2C1C CD2O1C CD32C CD33A 0.2416 1 180.00 ! +OD2C1C CD2O1C CD32C CD33A 0.2059 2 180.00 ! +OD2C1C CD2O1C CD32C CD33A 0.1496 3 180.00 ! +OD2C1C CD2O1C CD32C CD33A 0.0765 6 180.00 ! +HDP1C CD2O1C CD32C CD33A 0.2240 1 0.00 ! +HDP1C CD2O1C CD32C CD33A 0.2179 2 180.00 ! +HDP1C CD2O1C CD32C CD33A 0.3116 3 0.00 ! +HDP1C CD2O1C CD32C CD33A 0.0606 6 0.00 ! +!bald +OD2C1C CD2O1C CD32C CD32A 0.3296 1 180.00 ! +OD2C1C CD2O1C CD32C CD32A 0.1850 2 180.00 ! +OD2C1C CD2O1C CD32C CD32A 0.1420 3 180.00 ! +OD2C1C CD2O1C CD32C CD32A 0.0086 6 0.00 ! +HDP1C CD2O1C CD32C CD32A 0.2032 1 0.00 ! +HDP1C CD2O1C CD32C CD32A 0.0704 2 180.00 ! +HDP1C CD2O1C CD32C CD32A 0.2642 3 0.00 ! +HDP1C CD2O1C CD32C CD32A 0.0220 6 180.00 ! +!ibld +OD2C1C CD2O1C CD31C CD33A 0.3499 1 180.00 ! +OD2C1C CD2O1C CD31C CD33A 0.4616 2 180.00 ! +OD2C1C CD2O1C CD31C CD33A 0.3495 3 180.00 ! +OD2C1C CD2O1C CD31C CD33A 0.0181 6 0.00 ! +HDP1C CD2O1C CD31C CD33A 0.0438 1 180.00 ! +HDP1C CD2O1C CD31C CD33A 0.0154 2 180.00 ! +HDP1C CD2O1C CD31C CD33A 0.1205 3 0.00 ! +HDP1C CD2O1C CD31C CD33A 0.0017 6 0.00 ! +!carbonyls end +!! MGUAN/BGUAN fylin +CD2N1A ND2P1A CD32A HDA2C 0.000 3 0.00 ! ARG, c22 +HDP1B ND2P1A CD32A HDA2C 0.000 3 0.00 ! ARG, c22 +!DMP, lipids & DNA backbone +CD33A OD30B PD1A OD2C2B 0.8520 1 0.00 ! DMP, a&a +CD33A OD30B PD1A OD2C2B 0.3200 2 180.00 ! DMP, a&a +CD33A OD30B PD1A OD2C2B 0.0732 3 0.00 ! DMP, a&a +CD33A OD30B PD1A OD2C2B 0.1860 4 0.00 ! DMP, a&a +CD33A OD30B PD1A OD2C2B 0.0002 5 0.00 ! DMP, a&a +CD33A OD30B PD1A OD2C2B 0.0151 6 0.00 ! DMP, a&a +CD33C OD30B PD1A OD2C2B 0.8520 1 0.00 ! DMP, a&a +CD33C OD30B PD1A OD2C2B 0.3200 2 180.00 ! DMP, a&a +CD33C OD30B PD1A OD2C2B 0.0732 3 0.00 ! DMP, a&a +CD33C OD30B PD1A OD2C2B 0.1860 4 0.00 ! DMP, a&a +CD33C OD30B PD1A OD2C2B 0.0002 5 0.00 ! DMP, a&a +CD33C OD30B PD1A OD2C2B 0.0151 6 0.00 ! DMP, a&a +CD33A OD30B PD1A OD30B 0.6417 1 180.00 ! DMP, a&a +CD33A OD30B PD1A OD30B 0.7706 2 0.00 ! DMP, a&a +CD33A OD30B PD1A OD30B 0.1118 3 0.00 ! DMP, a&a +CD33A OD30B PD1A OD30B 0.0905 4 0.00 ! DMP, a&a +CD33A OD30B PD1A OD30B 0.0532 5 180.00 ! DMP, a&a +CD33A OD30B PD1A OD30B 0.0167 6 180.00 ! DMP, a&a +CD33C OD30B PD1A OD30B 0.6417 1 180.00 ! DMP, a&a +CD33C OD30B PD1A OD30B 0.7706 2 0.00 ! DMP, a&a +CD33C OD30B PD1A OD30B 0.1118 3 0.00 ! DMP, a&a +CD33C OD30B PD1A OD30B 0.0905 4 0.00 ! DMP, a&a +CD33C OD30B PD1A OD30B 0.0532 5 180.00 ! DMP, a&a +CD33C OD30B PD1A OD30B 0.0167 6 180.00 ! DMP, a&a +PD1A OD30B CD32A HDA2A 0.000 3 0.00 ! DMP, charmm27 +PD1A OD30B CD32B HDA2A 0.000 3 0.00 ! DMP, charmm27 +PD1A OD30B CD33A HDA3A 0.000 3 0.00 ! DMP, charmm27 +PD1A OD30B CD33C HDA3A 0.000 3 0.00 ! DMP, charmm27 +!phosphates +! MP_1 below, lipid and nucleic acid phosphodiester parameters in respective toppar files +CD33C OD30D PD1A OD2C2B 0.1000 3 0.00 ! MP_1 +CD33C OD30D PD1A OD31D 0.5000 3 0.00 ! MP_1 +CD33C OD30D PD1A OD31D 0.9500 2 0.00 ! +PD1A OD30D CD33C HDA3A 0.0000 3 0.00 ! MP_1 +OD30D PD1A OD31D HDP1A 0.2000 1 180.00 ! MP_1 +OD30D PD1A OD31D HDP1A 1.0000 2 0.00 ! +HDP1A OD31D PD1A OD2C2B 0.2000 3 0.00 ! MP_1 +HDP1A OD31D PD1A OD31D 0.3000 3 0.00 ! MP_0 specific, c36 +!phosphates end + +!sulfate, sulfonate, sulfamate, a&a +OD2C2B SD1A CD33C HDA3A 0.280 3 0.00 +SD1A OD30B CD33C HDA3A 0.200 3 0.00 +OD2C2B SD1A OD30B CD33C 0.200 3 0.00 +OD30E CD32A CD33A HDA3A 0.175 3 0.00 +CD32C ND2A2 SD1A OD2C2B 0.500 3 0.00 +SD1A ND2A2 CD32C HDA2A 0.200 3 0.00 +SD1A ND2A2 CD32C CD33C 0.500 3 0.00 +OD2C2B SD1A ND2A2 HDP1A 0.200 3 0.00 +ND2A2 CD32C CD33C HDA3A 0.200 3 0.00 +HDP1A ND2A2 CD32C CD33C 0.200 3 0.00 +HDA2A CD32C CD33C HDA3A 0.200 3 0.00 +CD33C ND2A2 SD1A OD2C2B 0.200 3 0.00 +SD1A ND2A2 CD33C HDA3A 0.200 3 0.00 + +! N-ethylacetamide, jal +CD2O1A ND2A2 CD32C CD33A 0.250 1 0.00 ! jal 03/26/18 manual opt +CD2O1A ND2A2 CD32C CD33A 0.350 2 0.00 ! jal 03/26/18 manual opt +ND2A2 CD32C CD33A HDA3A 0.100 3 0.00 ! jal 03/26/18 manual opt +HDP1A ND2A2 CD32C CD33A 0.550 1 0.00 ! jal 03/26/18 manual opt +HDP1A ND2A2 CD32C CD33A 0.250 3 0.00 ! jal 03/26/18 manual opt +! N-propylacetamide, jal +CD2O1A ND2A2 CD32C CD32A 0.250 1 0.00 ! jal 04/05/18 from NEA +CD2O1A ND2A2 CD32C CD32A 0.350 2 0.00 ! jal 04/05/18 from NEA +ND2A2 CD32C CD32A HDA2A 0.200 3 0.00 ! from GLN, alkanes +CD33A CD32A CD32C ND2A2 0.500 1 180.00 ! jal 04/05/18 manual opt +CD33A CD32A CD32C ND2A2 0.375 2 0.00 +CD33A CD32A CD32C ND2A2 0.250 3 0.00 +HDP1A ND2A2 CD32C CD32A 0.250 3 0.00 ! jal 04/05/18 from NEA + +IMPROPER +! +!V(improper) = Kpsi(psi - psi0)**2 +! +!Kpsi: kcal/mole/rad**2 +!psi0: degrees +!note that the second column of numbers (0) is ignored +! +OD2C3A CD32C OD31F CD2O3A 85.000 0 0.00 ! ACEH/CTP, PEML +CD2O1A CD32A ND2A2 OD2C1A 100.000 0 0.00 ! NMA/GLY +CD2O1A CD31C ND3A3 OD2C1A 0.000 0 0.00 ! Pro +CD2O1A CD32C ND3A3 OD2C1A 0.000 0 0.00 ! Pro +ND3A3 CD2O1A CD31C CD32A 0.000 0 0.00 ! Pro +CD2O1A CD31C ND2A1 OD2C1A 120.000 0 0.00 ! NTER +CD2O1A CD31A ND2A2 OD2C1A 120.000 0 0.00 ! NTER +CD2O1A CD32A ND3A3 OD2C1A 120.000 0 0.00 ! NTER +CD2O1A CD33C ND3A3 OD2C1A 120.000 0 0.00 ! NTER +OD2C2A CD31A OD2C2A CD2O2A 71.000 0 0.00 ! CTER +OD2C2A CD32A OD2C2A CD2O2A 71.000 0 0.00 ! ASP/GLU +OD2C2A CD33A OD2C2A CD2O2A 71.000 0 0.00 ! ACET +OD2C2A CD31C OD2C2A CD2O2A 71.000 0 0.00 ! CTER +OD2C2A CD32C OD2C2A CD2O2A 71.000 0 0.00 ! CTER, Gly +OD2C3A CD31C OD31F CD2O3A 85.000 0 0.00 ! ACEH/CTP, PEML +OD2C3A CD31A OD31F CD2O3A 85.000 0 0.00 ! ACEH/CTP, PEML +CD2O1A CD32C ND2A1 OD2C1A 90.000 0 0.00 ! ACEM/ASN +CD2O1A CD31C ND2A2 OD2C1A 37.200 0 0.00 ! ALAD, alanine dipeptide % +CD2O1A CD32C ND2A2 OD2C1A 100.000 0 0.00 ! NMA/GLY +CD2O1A CD33C ND2A2 OD2C1A 89.400 0 0.00 ! NMA/GLY +OD2C1A ND2A1 CD33C CD2O1A 90.000 0 0.00 ! ACEM, acetamide +ND2A1 HDP1A HDP1A CD2O1A 4.000 0 0.00 ! ACEM, acetamide +OD2C1A ND2A3 CD33C CD2O1A 60.000 0 0.00 ! DMA, N,N-dimethylacetamide +ND2A2 CD2O1A CD31C HDP1A 30.700 0 0.00 ! ALAD, alanine dipeptide +ND2A2 CD2O1A CD32C HDP1A 40.000 0 0.00 ! GLYD +ND2A2 CD2O1A CD33C HDP1A 35.600 0 0.00 ! NMA +CD2O2A OD2C2A OD2C2A CD33A 71.000 0 0.00 ! acetate +CD2O2A OD2C2A OD2C2A CD32A 71.000 0 0.00 ! acetate +CD2O2A OD2C2A OD2C2A CD32C 71.000 0 0.00 ! acetate +CD2O2A OD2C2A OD2C2A CD31A 71.000 0 0.00 ! acetate, CTER +CD2O2A OD2C2A OD2C2A CD31C 71.000 0 0.00 ! acetate, CTER +ND2R5A CD2R5A CD2R5B HDP1A 0.450 0 0.00 ! IMID, imidazole +ND2R5A CD2R5B CD2R5A HDP1A 0.450 0 0.00 ! IMID, imidazole +CD2R5A CD2R5A ND2R5B HDR5A 0.500 0 0.00 ! IMID, imidazole +CD2R5A ND2R5B CD2R5A HDR5A 0.500 0 0.00 ! IMID, imidazole +CD2R5B ND2R5A ND2R5B HDR5B 0.500 0 0.00 ! IMID, imidazole +CD2R5B ND2R5B ND2R5A HDR5B 0.500 0 0.00 ! IMID, imidazole +CD2R5A CD2R5A ND2R5A HDR5A 0.500 0 0.00 ! IMID, imidazole +CD2R5A ND2R5A CD2R5A HDR5A 0.500 0 0.00 ! IMID, imidazole +ND2R5C CD2R5E CD2R5D HDP1A 0.450 0 0.00 ! IMIM, from IMID (EH) +CD2R5D CD2R5D ND2R5C HDR5D 0.500 0 0.00 ! IMIM, from IMID (EH) +CD2R5E ND2R5C ND2R5C HDR5E 0.500 0 0.00 ! IMIM, from IMID (EH) +CD2N1A ND2P1A ND2P1A ND2P1A 40.000 0 0.00 ! GUAN, c22 +HDR5A ND2R5A CD2R5C CD2R5A 0.450 0 0.00 ! Pyrrole +HDR5A CD2R5C ND2R5A CD2R5A 0.450 0 0.00 ! Pyrrole +HDP1A CD2R5A CD2R5A ND2R5A 0.450 0 0.00 ! Pyrrole +HDR5C CD2R5A CD2R5C CD2R5C 0.450 0 0.00 ! Pyrrole +HDR5C CD2R5C CD2R5A CD2R5C 0.450 0 0.00 ! Pyrrole +HDP1A CD2R5A CD2R6D ND2R5A 0.450 0 0.00 ! INDO, indole +HDP1A CD2R6D CD2R5A ND2R5A 0.450 0 0.00 ! INDO, indole +CD2R6A CD2R6A CD2R6D HDR6A 0.450 0 0.00 ! INDO, indole +HDR6A CD2R6A CD2R6D CD2R6A 0.450 0 0.00 ! INDO, indole +HDR5C CD2R6D CD2R5A CD2R5C 0.450 0 0.00 ! INDO, indole +HDR5C CD2R5A CD2R6D CD2R5C 0.450 0 0.00 ! INDO, indole +ND2R5A CD2R6F CD2R5B HDP1A 0.450 0 0.00 ! PUR0/1, purine +ND2R5A CD2R5B CD2R6F HDP1A 0.450 0 0.00 ! PUR0/1, purine +CD2R6F CD2R6F CD2R6B ND2R5A 20.000 0 0.00 ! PUR1, purine +CD2R6F CD2R6B CD2R6F ND2R5A 20.000 0 0.00 ! PUR1, purine +CD2R6F CD2R6F ND2R6B ND2R5B 10.000 0 0.00 ! PUR1, purine +CD2R6F ND2R6B CD2R6F ND2R5B 10.000 0 0.00 ! PUR1, purine +CD2R6F CD2R6F CD2R6B ND2R5B 20.000 0 0.00 ! PUR0, purine +CD2R6F CD2R6B CD2R6F ND2R5B 20.000 0 0.00 ! PUR0, purine +CD2R6F CD2R6F ND2R6B ND2R5A 10.000 0 0.00 ! PUR0, purine +CD2R6F ND2R6B CD2R6F ND2R5A 10.000 0 0.00 ! PUR0, purine +CD2O4A ND2R6B ND2R6B OD2C1B 80.000 0 0.00 ! CYT, jal +CD2O4A ND2R6C ND2R6C OD2C1B 80.000 0 0.00 ! CYT, jal +CD2O4A ND2R6C ND2R6B OD2C1B 80.000 0 0.00 ! CYT, jal +CD2R6B ND2R6B CD2R6J ND2B1 60.000 0 0.00 ! CYT, jal +ND2R6B CD2R6H CD2O4A HDP1A 1.000 0 0.00 ! CYT, jal +ND2R6C CD2R6H CD2O4A HDP1A 1.000 0 0.00 ! CYT, jal +ND2R6C CD2R6H CD2O4A CD33A 14.000 0 0.00 ! CYT, jal +CD2O4A ND2R6B ND2R6C OD2C1B 110.000 0 0.00 ! THY, jal +CD2O4A ND2R6C CD2R6J OD2C1B 90.000 0 0.00 ! THY, jal +CD2R6J CD2O4A CD2R6H CD33A 14.000 0 0.00 ! THY, jal +CD2R6C ND2R6B ND2R6C ND2B1 40.000 0 0.00 ! GUA, cmb 04/10 +CD2O4A ND2R6C CD2R6F OD2C1B 90.000 0 0.00 ! GUA, jal +ND2B1 HDP1A CD2R6C HDP1A 6.000 0 0.00 ! GUA, cmb 04/10 +OD2C3A CD33A OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD32A OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD33C OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD32C OD30C CD2O3A 85.000 0 0.00 ! MAS +OD2C3A CD31C OD30C CD2O3A 85.000 0 0.00 ! MAS, CT1 +CD2O3A OD31F CD33C OD2C3A 85.000 0 0.00 ! ACEH, PEML +!alkenes +!!! alkenes, canonical ordering, PC & ADM 07/2022 +CD2C1A CD2C1A CD32A HD2C1A 2.000 0 0.00 ! alkenes, pc & adm updated 06/2022 +CD2C1A CD2C1B CD32A HD2C1A 2.000 0 0.00 ! alkenes, pc 06/2022 +CD2C1A CD32A CD2C1A HD2C1A 2.000 0 0.00 ! alkenes, pc & adm updated 06/2022 +CD2C1A CD32A CD2C1B HD2C1A 2.000 0 0.00 ! alkenes, pc 06/2022 +CD2C1A CD2C1A CD33A HD2C1A 2.000 0 0.00 ! alkenes, pc & adm updated 06/2022 +CD2C1A CD2C1B CD33A HD2C1A 2.000 0 0.00 ! alkenes, PRPE; pc 06/2022 +!alkene end +!carbonyls +CD2O1D CD33C CD33C OD2C1D 98.000 0 0.00 ! acetone +CD2O1D CD33C CD32C OD2C1D 93.000 0 0.00 ! +CD2O1D CD32C CD32C OD2C1D 95.000 0 0.00 ! +CD2O1C HDP1C CD33C OD2C1D 75.000 0 0.00 ! ethanal +CD2O1C HDP1C CD32C OD2C1D 71.300 0 0.00 ! +CD2O1C HDP1C CD33C OD2C1C 75.000 0 0.00 ! ethanal +CD2O1C HDP1C CD32C OD2C1C 71.300 0 0.00 ! +CD2O1C HDP1C CD31C OD2C1C 71.300 0 0.00 ! +CD2O1C HDP1C CD31G OD2C1C 71.300 0 0.00 ! +CD2O1D CD32F CD31G OD2C1D 93.000 0 0.00 ! +!carbonyls end +CD2O1C ND2A1 OD2C1D HDP1C 70.000 0 0.00 ! FORM, fylin + +CMAP + +!! drude2013e ! ps. this section was updated by Jing in 2017july.str +!! CMAP pure dipeptide cmap +!! alanine-based map, rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ level +!! transfer to following 2 CMAP surfaces for +!! residue adjacent to Pro and C-terminal CT2 patch +! +!!rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ +!CD2O1A ND2A2 CD31C CD2O1A ND2A2 CD31C CD2O1A ND2A2 24 +! +!! insertion 1 +!! alanine map, pure RIMP2 MP2-CBS dipeptide +!! CD2O1A ND2A2 CD31C CD2O1A ND2A2 CD31C CD2O1A ND2A2 24 + +! alanine map, pure RIMP2 MP2-CBS dipeptide, for sensitivity analysis +CD2O1A ND2A2 CD31C CD2O1A ND2A2 CD31C CD2O1A ND2A2 24 + +!-180 + -2.78 -2.17 -1.32 -0.14 2.13 + 3.19 3.62 2.72 2.29 -1.03 + -0.50 -5.26 -9.40 -9.79 -8.76 + -6.65 -4.16 -2.22 -1.18 -0.79 + -2.66 -3.61 -3.49 -3.22 + +!-165 + -2.34 -1.92 -1.21 -0.09 2.18 + 3.23 3.55 2.51 2.25 -0.90 + -1.95 -6.68 -8.92 -9.05 -7.94 + -5.86 -3.55 -1.79 -0.82 -0.36 + -2.10 -2.93 -2.77 -2.59 + +!-150 + -2.60 -2.27 -1.57 -0.42 1.86 + 2.84 2.94 1.89 1.79 1.06 + -3.66 -7.49 -8.83 -8.82 -7.64 + -5.59 -3.39 -1.78 -0.89 -0.41 + -2.10 -2.92 -2.80 -2.73 + +!-135 + -3.20 -2.77 -1.96 -0.76 1.48 + 2.24 2.12 1.16 1.32 -0.68 + -5.19 -8.01 -9.16 -9.03 -7.74 + -5.66 -3.59 -2.18 -2.35 -1.84 + -2.55 -3.42 -3.37 -3.34 + +!-120 + -3.61 -3.07 -2.23 -1.11 0.94 + 1.50 1.39 0.62 1.82 -2.01 + -5.96 -8.31 -9.27 -8.96 -7.51 + -5.46 -3.69 -3.52 -2.68 -2.14 + -2.88 -3.84 -3.86 -3.83 + +!-105 + -3.56 -3.08 -2.37 -1.42 0.51 + 1.08 1.13 0.64 1.24 -2.48 + -5.87 -7.93 -8.62 -7.99 -6.36 + -4.74 -4.41 -3.38 -2.47 -1.89 + -2.69 -3.72 -3.80 -3.78 + +!-90 + -3.24 -2.93 -2.40 -1.55 0.41 + 1.12 1.41 1.23 0.19 -3.29 + -6.25 -7.95 -8.19 -7.09 -5.85 + -4.82 -3.79 -2.81 -1.94 -1.31 + -2.12 -3.20 -3.32 -3.35 + +!-75 + -3.21 -3.09 -2.66 -1.79 0.32 + 1.24 1.83 1.73 -0.77 -3.94 + -6.47 -7.62 -7.25 -6.52 -6.09 + -4.53 -3.69 -2.66 -1.72 -1.04 + -1.78 -2.87 -3.03 -3.15 + +!-60 + -3.88 -3.83 -3.30 -2.22 0.08 + 1.19 2.01 1.39 -1.04 -3.77 + -5.64 -6.21 -6.14 -6.37 -6.45 + -5.05 -4.08 -2.88 -1.86 -1.24 + -2.06 -3.23 -3.45 -3.67 + +!-45 + -4.88 -4.61 -3.72 -2.42 -0.08 + 1.23 1.87 0.56 -1.62 -3.68 + -4.97 -5.64 -6.56 -7.31 -7.49 + -5.88 -4.52 -3.04 -2.02 -1.67 + -2.87 -4.27 -4.54 -4.73 + +!-30 + -5.52 -4.82 1.06 -1.39 -0.25 + 0.67 0.68 -0.37 -1.99 -3.49 + -4.75 -6.45 -7.98 -8.87 -8.78 + -6.54 -4.67 -2.94 -2.15 -2.39 + -4.04 -5.48 -5.60 -5.64 + +!-15 + -4.61 -3.52 -3.09 -2.12 -1.04 + -0.25 -0.01 -0.60 -1.83 -3.28 + -5.72 -8.15 -9.87 -10.50 -9.64 + -6.67 -4.40 -2.88 -3.05 -3.64 + -5.17 -5.31 -5.25 -5.10 + +!0 + -2.86 -2.91 -2.70 -2.00 -1.15 + -0.22 0.41 0.01 -1.18 -4.12 + -7.31 -9.81 -11.13 -10.83 -9.23 + -7.02 -5.33 -5.35 -5.35 -5.61 + -5.70 -5.65 -5.58 -5.30 + +!15 + -2.79 -2.78 -2.49 -1.81 -0.72 + 0.70 1.60 1.03 -1.61 -5.00 + -7.99 -9.83 -10.18 -9.36 -7.79 + -6.39 -6.51 -6.20 -5.87 -5.68 + -5.62 -5.73 -2.99 -3.18 + +!30 + -2.95 -2.69 -2.20 -1.26 0.25 + 1.86 2.31 0.86 -1.88 -4.87 + -7.20 -8.27 -8.32 -7.63 -6.82 + -7.13 -6.97 -6.14 -5.27 -4.88 + -4.93 -4.53 -3.98 -3.36 + +!45 + -2.47 -2.02 -1.30 -0.13 1.43 + 2.63 2.50 0.91 -1.54 -4.06 + -5.83 -6.70 -6.90 -6.84 -7.38 + -7.66 -6.81 -5.29 -4.12 -3.96 + -4.19 -4.03 -3.57 -2.99 + +!60 + -1.25 -0.74 0.09 1.28 2.62 + 3.40 2.98 1.44 -0.73 -2.95 + -4.59 -5.66 -6.41 -7.39 -8.33 + -7.96 -6.35 -4.50 -3.43 -3.36 + -3.27 -2.92 -2.39 -1.78 + +!75 + -0.16 0.30 1.11 2.22 3.39 + 4.03 3.55 2.12 0.11 -2.04 + -3.89 -5.50 -7.16 -8.81 -9.19 + -8.08 -6.00 -4.02 -2.95 -2.73 + -2.34 -1.83 -1.24 -0.63 + +!90 + 0.29 0.66 1.37 2.36 3.41 + 4.08 3.65 2.32 0.38 -1.92 + -4.25 -6.59 -8.83 -10.02 -9.74 + -8.09 -5.63 -3.67 -3.04 -2.53 + -1.95 -1.36 -0.75 -0.13 + +!105 + 0.03 0.38 0.99 1.86 2.79 + 3.49 3.34 2.02 0.00 -2.60 + -5.53 -8.34 -10.30 -10.97 -10.21 + -7.96 -5.13 -3.94 -3.34 -2.66 + -2.04 -1.50 -0.97 -0.42 + +!120 + -1.10 -0.52 0.19 1.07 1.94 + 2.63 2.77 1.74 -0.48 -3.64 + -7.09 -9.91 -11.60 -11.95 -10.75 + -6.34 -5.66 -4.68 -3.69 -2.88 + -2.38 -2.16 -1.99 -1.65 + +!135 + -2.52 -1.61 -0.63 0.42 1.37 + 2.09 2.35 1.48 -0.97 -4.53 + -8.17 -10.99 -12.63 -7.93 -9.51 + -8.62 -6.90 -5.18 -3.82 -3.02 + -2.92 -3.19 -3.38 -3.18 + +!150 + -3.18 -2.23 -1.08 0.18 1.32 + 2.18 2.54 1.72 -0.81 -4.47 + -8.08 -10.84 -8.00 -11.49 -11.66 + -9.79 -7.28 -5.07 -3.65 -3.22 + -3.41 -3.79 -4.00 -3.81 + +!165 + -3.69 -2.89 -1.85 -0.57 1.70 + 2.69 3.13 2.32 -0.17 -3.71 + -7.14 -5.73 -10.04 -12.44 -11.66 + -9.53 -7.05 -5.14 -4.26 -4.21 + -4.30 -4.47 -4.50 -4.25 + + +! for C-terminal CT2 patch +!rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ +CD2O1A ND2A2 CD31C CD2O1A ND2A2 CD31C CD2O1A ND2A1 24 + +! insertion 2 +! alanine map, pure RIMP2 MP2-CBS dipeptide +! 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glycine map +! for GLY with amidated C-terminus (CT2G) +! rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ +CD2O1A ND2A2 CD32C CD2O1A ND2A2 CD32C CD2O1A ND2A1 24 + +!-180 + -3.21 -2.92 -2.05 -0.77 0.55 + 1.52 1.80 0.96 -1.13 -3.98 + -6.62 -8.29 -8.55 -5.43 -6.62 + -3.98 -1.13 0.97 1.80 1.52 + 0.55 -0.77 -2.05 -2.92 + +!-165 + -3.53 -3.47 -2.68 -1.34 0.14 + 1.30 1.68 0.82 -1.26 -3.99 + -6.43 -7.78 -6.37 -3.25 -6.93 + -4.19 -1.30 0.83 1.72 1.57 + 0.72 -0.54 -1.89 -2.97 + +!-150 + -4.34 -4.35 -3.48 -1.96 -0.29 + 0.95 1.18 0.19 -1.70 -4.11 + -6.13 -6.51 -4.46 -9.33 -7.42 + -4.60 -1.69 0.44 1.37 1.31 + 0.52 -0.78 -2.27 -3.57 + +!-135 + -5.18 -5.15 -4.15 -2.51 -0.86 + 0.16 0.22 -0.61 -2.20 -4.14 + -5.51 -10.04 -10.61 -9.83 -7.81 + -4.94 -2.06 -0.05 0.88 0.90 + 0.12 -1.25 -2.88 -4.33 + +!-120 + -5.65 -5.58 -4.60 -3.07 -1.60 + -0.68 -0.52 -1.14 -2.38 -3.88 + -8.55 -10.35 -10.74 -9.79 -7.63 + -4.79 -2.16 -0.37 0.59 0.67 + -0.11 -1.55 -3.27 -4.79 + +!-105 + -5.73 -5.75 -4.91 -3.54 -2.15 + -1.18 -0.87 -1.23 -2.18 -5.66 + -8.60 -10.12 -10.25 -9.03 -6.77 + -4.31 -2.14 -0.49 0.56 0.73 + -0.06 -1.53 -3.28 -4.83 + +!-90 + -5.82 -6.00 -5.33 -4.05 -2.63 + -1.52 -0.98 -1.04 -2.79 -5.90 + -8.38 -9.56 -9.29 -7.75 -5.88 + -4.01 -2.15 -0.54 0.52 0.76 + 0.01 -1.48 -3.25 -4.83 + +!-75 + -6.39 -6.76 -6.25 -4.98 -3.41 + -2.04 -1.14 -0.92 -3.22 -6.01 + -8.05 -8.72 -7.99 -6.86 -5.75 + -4.34 -2.67 -1.01 0.11 0.40 + -0.30 -1.80 -3.61 -5.26 + +!-60 + -7.51 -8.03 -7.49 -5.97 -4.14 + -2.56 -1.41 -1.71 -3.72 -6.05 + -7.50 -7.70 -7.38 -7.20 -6.64 + -5.42 -3.61 -1.72 -0.46 -0.20 + -1.02 -2.63 -4.50 -6.23 + +!-45 + -8.62 -8.95 -8.00 -6.17 -4.42 + -2.94 -1.96 -2.58 -4.28 -6.00 + -6.97 -7.46 -8.20 -8.57 -8.13 + -6.72 -4.48 -2.23 -0.84 -0.76 + -1.89 -3.73 -5.62 -7.34 + +!-30 + -9.06 -8.81 -7.33 -4.52 0.14 + -3.58 -2.91 -3.41 -4.68 -5.96 + -7.09 -8.71 -10.04 -10.50 -9.82 + -7.86 -5.05 -2.42 -1.09 -1.44 + -2.92 -4.74 -6.50 -8.09 + +!-15 + -8.59 -6.27 -1.91 -5.03 -4.72 + -3.75 -3.33 -3.71 -4.80 -6.22 + -8.64 -10.90 -12.29 -12.45 -11.12 + -8.41 -5.15 -2.57 -1.93 -2.55 + -3.90 -5.42 -6.99 -8.29 + +!0 + -4.39 -7.37 -7.10 -5.76 -4.47 + -3.46 -2.95 -3.43 -4.72 -7.64 + -10.64 -12.82 -13.69 -12.82 -10.64 + -7.64 -4.72 -3.43 -2.95 -3.46 + -4.47 -5.76 -7.11 -7.37 + +!15 + -8.59 -8.29 -6.99 -5.42 -3.90 + -2.55 -1.93 -2.57 -5.15 -8.41 + -11.12 -12.45 -12.29 -10.90 -8.64 + -6.22 -4.80 -3.71 -3.33 -3.75 + -4.72 -5.03 -1.91 -6.27 + +!30 + -9.06 -8.09 -6.50 -4.74 -2.92 + -1.44 -1.09 -2.42 -5.05 -7.86 + -9.82 -10.50 -10.04 -8.71 -7.09 + -5.96 -4.68 -3.41 -2.91 -3.58 + -0.02 -4.52 -7.33 -8.81 + +!45 + -8.62 -7.34 -5.62 -3.73 -1.89 + -0.76 -0.84 -2.23 -4.48 -6.72 + -8.13 -8.57 -8.20 -7.46 -6.97 + -6.00 -4.28 -2.58 -1.96 -2.94 + -4.42 -6.17 -8.00 -8.95 + +!60 + -7.51 -6.23 -4.50 -2.63 -1.02 + -0.20 -0.46 -1.72 -3.61 -5.42 + -6.64 -7.20 -7.38 -7.70 -7.50 + -6.05 -3.72 -1.71 -1.41 -2.56 + -4.14 -5.97 -7.49 -8.03 + +!75 + -6.39 -5.26 -3.61 -1.80 -0.30 + 0.40 0.11 -1.01 -2.67 -4.34 + -5.75 -6.86 -7.99 -8.72 -8.05 + -6.01 -3.22 -0.92 -1.14 -2.04 + -3.41 -4.98 -6.25 -6.76 + +!90 + -5.83 -4.83 -3.25 -1.48 0.01 + 0.76 0.52 -0.54 -2.15 -4.01 + -5.88 -7.75 -9.29 -9.56 -8.38 + -5.90 -2.79 -1.04 -0.98 -1.52 + -2.63 -4.05 -5.33 -6.00 + +!105 + -5.73 -4.83 -3.28 -1.53 -0.06 + 0.73 0.56 -0.49 -2.14 -4.31 + -6.77 -9.03 -10.25 -10.12 -8.60 + -5.66 -2.18 -1.23 -0.87 -1.18 + -2.15 -3.54 -4.91 -5.75 + +!120 + -5.65 -4.79 -3.27 -1.55 -0.11 + 0.67 0.59 -0.37 -2.16 -4.79 + -7.63 -9.79 -10.74 -10.35 -8.55 + -3.88 -2.38 -1.14 -0.52 -0.68 + -1.60 -3.07 -4.60 -5.58 + +!135 + -5.19 -4.33 -2.88 -1.25 0.12 + 0.90 0.88 -0.05 -2.06 -4.94 + -7.81 -9.83 -10.61 -10.04 -5.51 + -4.14 -2.20 -0.61 0.22 0.16 + -0.86 -2.51 -4.15 -5.15 + +!150 + -4.34 -3.57 -2.27 -0.78 0.52 + 1.31 1.37 0.44 -1.69 -4.60 + -7.42 -9.33 -4.46 -6.51 -6.13 + -4.11 -1.70 0.19 1.18 0.95 + -0.29 -1.96 -3.48 -4.35 + +!165 + -3.53 -2.97 -1.89 -0.54 0.72 + 1.57 1.72 0.83 -1.30 -4.19 + -6.93 -3.25 -6.37 -7.78 -6.43 + -3.99 -1.26 0.82 1.68 1.30 + 0.14 -1.34 -2.68 -3.47 + + +! glycine map +! for GLY adjacent to N-terminal PRO +! rimp2/cc-pVTZ/VQZ/CBS//mp2/aug-cc-pVDZ +CD2O1A ND2A2 CD32C CD2O1A ND2A2 CD32C CD2O1A ND3A3 24 + +!-180 + -3.21 -2.92 -2.05 -0.77 0.55 + 1.52 1.80 0.96 -1.13 -3.98 + -6.62 -8.29 -8.55 -5.43 -6.62 + -3.98 -1.13 0.97 1.80 1.52 + 0.55 -0.77 -2.05 -2.92 + +!-165 + -3.53 -3.47 -2.68 -1.34 0.14 + 1.30 1.68 0.82 -1.26 -3.99 + -6.43 -7.78 -6.37 -3.25 -6.93 + -4.19 -1.30 0.83 1.72 1.57 + 0.72 -0.54 -1.89 -2.97 + +!-150 + -4.34 -4.35 -3.48 -1.96 -0.29 + 0.95 1.18 0.19 -1.70 -4.11 + -6.13 -6.51 -4.46 -9.33 -7.42 + -4.60 -1.69 0.44 1.37 1.31 + 0.52 -0.78 -2.27 -3.57 + +!-135 + -5.18 -5.15 -4.15 -2.51 -0.86 + 0.16 0.22 -0.61 -2.20 -4.14 + -5.51 -10.04 -10.61 -9.83 -7.81 + -4.94 -2.06 -0.05 0.88 0.90 + 0.12 -1.25 -2.88 -4.33 + +!-120 + -5.65 -5.58 -4.60 -3.07 -1.60 + -0.68 -0.52 -1.14 -2.38 -3.88 + -8.55 -10.35 -10.74 -9.79 -7.63 + -4.79 -2.16 -0.37 0.59 0.67 + -0.11 -1.55 -3.27 -4.79 + +!-105 + -5.73 -5.75 -4.91 -3.54 -2.15 + -1.18 -0.87 -1.23 -2.18 -5.66 + -8.60 -10.12 -10.25 -9.03 -6.77 + -4.31 -2.14 -0.49 0.56 0.73 + -0.06 -1.53 -3.28 -4.83 + +!-90 + -5.82 -6.00 -5.33 -4.05 -2.63 + -1.52 -0.98 -1.04 -2.79 -5.90 + -8.38 -9.56 -9.29 -7.75 -5.88 + -4.01 -2.15 -0.54 0.52 0.76 + 0.01 -1.48 -3.25 -4.83 + +!-75 + -6.39 -6.76 -6.25 -4.98 -3.41 + -2.04 -1.14 -0.92 -3.22 -6.01 + -8.05 -8.72 -7.99 -6.86 -5.75 + -4.34 -2.67 -1.01 0.11 0.40 + -0.30 -1.80 -3.61 -5.26 + +!-60 + -7.51 -8.03 -7.49 -5.97 -4.14 + -2.56 -1.41 -1.71 -3.72 -6.05 + -7.50 -7.70 -7.38 -7.20 -6.64 + -5.42 -3.61 -1.72 -0.46 -0.20 + -1.02 -2.63 -4.50 -6.23 + +!-45 + -8.62 -8.95 -8.00 -6.17 -4.42 + -2.94 -1.96 -2.58 -4.28 -6.00 + -6.97 -7.46 -8.20 -8.57 -8.13 + -6.72 -4.48 -2.23 -0.84 -0.76 + -1.89 -3.73 -5.62 -7.34 + +!-30 + -9.06 -8.81 -7.33 -4.52 0.14 + -3.58 -2.91 -3.41 -4.68 -5.96 + -7.09 -8.71 -10.04 -10.50 -9.82 + -7.86 -5.05 -2.42 -1.09 -1.44 + -2.92 -4.74 -6.50 -8.09 + +!-15 + -8.59 -6.27 -1.91 -5.03 -4.72 + -3.75 -3.33 -3.71 -4.80 -6.22 + -8.64 -10.90 -12.29 -12.45 -11.12 + -8.41 -5.15 -2.57 -1.93 -2.55 + -3.90 -5.42 -6.99 -8.29 + +!0 + -4.39 -7.37 -7.10 -5.76 -4.47 + -3.46 -2.95 -3.43 -4.72 -7.64 + -10.64 -12.82 -13.69 -12.82 -10.64 + -7.64 -4.72 -3.43 -2.95 -3.46 + -4.47 -5.76 -7.11 -7.37 + +!15 + -8.59 -8.29 -6.99 -5.42 -3.90 + -2.55 -1.93 -2.57 -5.15 -8.41 + -11.12 -12.45 -12.29 -10.90 -8.64 + -6.22 -4.80 -3.71 -3.33 -3.75 + -4.72 -5.03 -1.91 -6.27 + +!30 + -9.06 -8.09 -6.50 -4.74 -2.92 + -1.44 -1.09 -2.42 -5.05 -7.86 + -9.82 -10.50 -10.04 -8.71 -7.09 + -5.96 -4.68 -3.41 -2.91 -3.58 + -0.02 -4.52 -7.33 -8.81 + +!45 + -8.62 -7.34 -5.62 -3.73 -1.89 + -0.76 -0.84 -2.23 -4.48 -6.72 + -8.13 -8.57 -8.20 -7.46 -6.97 + -6.00 -4.28 -2.58 -1.96 -2.94 + -4.42 -6.17 -8.00 -8.95 + +!60 + -7.51 -6.23 -4.50 -2.63 -1.02 + -0.20 -0.46 -1.72 -3.61 -5.42 + -6.64 -7.20 -7.38 -7.70 -7.50 + -6.05 -3.72 -1.71 -1.41 -2.56 + -4.14 -5.97 -7.49 -8.03 + +!75 + -6.39 -5.26 -3.61 -1.80 -0.30 + 0.40 0.11 -1.01 -2.67 -4.34 + -5.75 -6.86 -7.99 -8.72 -8.05 + -6.01 -3.22 -0.92 -1.14 -2.04 + -3.41 -4.98 -6.25 -6.76 + +!90 + -5.83 -4.83 -3.25 -1.48 0.01 + 0.76 0.52 -0.54 -2.15 -4.01 + -5.88 -7.75 -9.29 -9.56 -8.38 + -5.90 -2.79 -1.04 -0.98 -1.52 + -2.63 -4.05 -5.33 -6.00 + +!105 + -5.73 -4.83 -3.28 -1.53 -0.06 + 0.73 0.56 -0.49 -2.14 -4.31 + -6.77 -9.03 -10.25 -10.12 -8.60 + -5.66 -2.18 -1.23 -0.87 -1.18 + -2.15 -3.54 -4.91 -5.75 + +!120 + -5.65 -4.79 -3.27 -1.55 -0.11 + 0.67 0.59 -0.37 -2.16 -4.79 + -7.63 -9.79 -10.74 -10.35 -8.55 + -3.88 -2.38 -1.14 -0.52 -0.68 + -1.60 -3.07 -4.60 -5.58 + +!135 + -5.19 -4.33 -2.88 -1.25 0.12 + 0.90 0.88 -0.05 -2.06 -4.94 + -7.81 -9.83 -10.61 -10.04 -5.51 + -4.14 -2.20 -0.61 0.22 0.16 + -0.86 -2.51 -4.15 -5.15 + +!150 + -4.34 -3.57 -2.27 -0.78 0.52 + 1.31 1.37 0.44 -1.69 -4.60 + -7.42 -9.33 -4.46 -6.51 -6.13 + -4.11 -1.70 0.19 1.18 0.95 + -0.29 -1.96 -3.48 -4.35 + +!165 + -3.53 -2.97 -1.89 -0.54 0.72 + 1.57 1.72 0.83 -1.30 -4.19 + -6.93 -3.25 -6.37 -7.78 -6.43 + -3.99 -1.26 0.82 1.68 1.30 + 0.14 -1.34 -2.68 -3.47 + +! 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DMP, nucleic acids +OD30BN 0.0 -0.0200 1.7500 ! DMP, nucleic acids +PD1AN 0.0 -0.3200 1.9000 ! DMP, nucleic acids +! + +!! Hydrogens +HDP1A 0.0 -0.0100 0.4000 ! polar hydrogen, adm jr. and va +HDP1B 0.0 -0.0100 0.7500 ! MGUAN/GUAN/NC3/NC2/NC1/NH4, fylin 2018 +HDP1C 0.0 -0.0650 0.9500 ! aldehydes +HDA1A 0.0 -0.0200 1.3400 ! IBUT, isobutane, exp. dHvap/MV, VA, 10/07 +HDA1C 0.0 -0.0460 0.9250 ! NC4, EH 2007, tetramethylammonium H atoms +HDA1R5 0.0 -0.0450 1.3400 ! TF2M, cmb. From JPCB 109, 18988. +HDA2A 0.0 -0.0210 1.3400 ! PROP, propane, exp. dHvap/MV, VA, 10/07 +HDA2C 0.0 -0.0460 0.9250 ! NC4, EH 2007 +HDA2E 0.0 -0.0350 1.3400 ! THP, cmb 11/08 +HDA2R5 0.0 -0.0350 1.3000 ! CPEN, cyclopentane, MD sim., 8/06 viv +HDA3A 0.0 -0.0240 1.3400 ! ETHA, ethane, yin and mackerell, 4/98 +HDA3B 0.0 -0.0350 1.3400 ! special methyl H for MEOH, methanol +HDA3C 0.0 -0.0460 0.9250 ! NC4, EH 2007 +HDR5A 0.0 -0.0250 1.1500 ! IMID, imidazole (HG, HD1 atoms), PYRR on C removed from N, fylin 2016 +HDR5B 0.0 -0.0250 1.1000 ! IMID, imidazole (HE2 polar H atom on C between two Ns), fylin2016 +HDR5C 0.0 -0.0360 1.1800 ! PYRR, pyrrole, on C adjacent to N +HDR5D 0.0 -0.0350 0.7000 ! TESTING FOR IMIM +HDR5E 0.0 -0.1000 0.5500 ! TESTING FOR IMIM +HDR6A 0.0 -0.0300 1.0500 ! BENZ, benzene (standard aromatic) +HDR6B 0.0 -0.0700 0.8000 ! PYR, pyridine (on carbon adjacent to N) +HDR6C 0.0 -0.0700 0.8000 ! PYRM, pyrimidine (on carbon between 2 Ns) +HDW 0.0 -0.0000 0.0000 ! SWM4-NDP water, GL, 2005, also for SWM6-NDP +HD2C1A 0.0 -0.0371 1.1070 ! internal alkene H, DL based parameters pc; 08/2021 +HD2C1B 0.0 -0.0375 1.3388 ! terminal alkene H, DL based parameters pc; 08/2021 +!! Carbons +CD2O1A 0.0 -0.0500 1.7750 ! carbonyl C, amides +CD2O1C 0.0 -0.1150 1.6800 ! carbonyl C, aldehydes +CD2O1D 0.0 -0.1350 1.7500 ! carbonyl C, ketones +CD2O2A 0.0 -0.4300 1.4700 ! ACET, fylin, mar27, 2018 +CD2O3A 0.0 -0.0300 1.7750 ! carbonyl C, lipid esters +CD2O4A 0.0 -0.0960 1.6730 ! nucleic acids, jal +CD2C1A 0.0 -0.0676 2.2680 ! internal alkene C, DL based parameters pc; 08/2021 +CD2C1B 0.0 -0.0649 2.0542 ! terminal alkene C, DL based parameters pc; 08/2021 +CD2N1A 0.0 -0.4750 1.8000 ! MGUAN/GUAN, fylin, mar27 2018 +CD2R5A 0.0 -0.1100 2.1300 ! IMID, imidazole (N acceptor), fylin 2016 +CD2R5B 0.0 -0.0930 1.9800 ! IMID, imidazole, CE1 +CD2R5C 0.0 -0.0500 2.0900 ! too big (balance with its H) PYRR, pyrrole +CD2R5D 0.0 -0.0500 1.8000 ! IMIM, fylin 2018 +CD2R5E 0.0 -0.1000 1.8500 ! IMIM, fylin 2018 +CD2R5F 0.0 -0.1430 2.0920 ! nucleic acids, jal +CD2R6A 0.0 -0.0690 2.0900 ! BENZ, benzene +CD2R6B 0.0 -0.1190 1.8700 ! PYR, pyridine (adjacent to N), jal +CD2R6C 0.0 -0.1070 1.8690 ! PYRM, pyrimidine (between 2 Ns), jal +CD2R6D 0.0 -0.0380 1.9000 ! INDO, indole: 5,6 membered ring bisector C +CD2R6F 0.0 -0.0780 1.8220 ! PUR0/1, purine: 5,6 membered ring bisector C, jal +CD2R6H 0.0 -0.1070 1.9700 ! CYT/THY/URA, jal +CD2R6I 0.0 -0.7800 1.5500 ! PHET, fylin, mar27, 2018 +CD2R6J 0.0 -0.1040 2.1290 ! nucleic acids, jal +CD30A 0.0 -0.0200 2.2000 0.0 -0.01 1.9 ! NEOP, neopentane, by analogy from CD31A, needs work +CD30FA 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! from, glycerol, furanoses, anomeric C1 +CD30HA 0.0 -0.0600 1.9000 0.0 -0.01 1.9 ! hexopyranose, C2, BNE5AC, from CD31HA +CD31A 0.0 -0.0220 2.2000 0.0 -0.01 1.9 ! IBUT, isobutane, dHvap/MV, VA, 10/07 +CD31C 0.0 -0.0320 1.8000 0.0 -0.01 1.9 ! NMA/MAS/ACEH PEML +CD31DC 0.0 -0.0320 1.8000 0.0 -0.01 1.9 ! for D-amino acids, jal +CD31FA 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! from, glycerol, furanoses, anomeric C1 +CD31FB 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! from, glycerol, furanoses, C2,C3 +CD31FC 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! from THF, furanoses, C4 +CD31G 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! glycerol, xhe +CD315A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! CPNM, cmb, from JPCB 109, 18988 +CD315B 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! TF2M, cmb, from JPCB 109, 18988 +CD316A 0.0 -0.0320 2.0000 0.0 -0.01 1.9 ! CHXM, cmb, from JPCB 109, 18988 +CD31HA 0.0 -0.0600 1.9000 0.0 -0.01 1.9 ! hexopyranose, C1, glucose diffusion, Carb Res, 2018 +CD31HB 0.0 -0.0600 1.9000 0.0 -0.01 1.9 ! hexopyranose, C2,C3,C4, glucose diffusion, Carb Res, 2018 +CD31HC 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! hexopyranoses, C5 +CD32A 0.0 -0.0560 2.1000 0.0 -0.01 1.9 ! PROP, propane, VA, 10/07 +CD32B 0.0 -0.0560 2.1000 0.0 -0.01 1.9 ! for GLU, from CD32A +CD32C 0.0 -0.0560 1.8100 0.0 -0.01 1.9 ! NMA/MAS/ACEH PEML +CD32HB 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! hexopyranoses, C3, ANE5AC, from CD326B +CD32HC 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! hexopyranoses, C5, AXYL, BXYL, from CD326B +CD32E 0.0 -0.0540 2.0200 0.0 -0.01 1.9 ! DMEE, ethers, cmb 11/08 +CD32F 0.0 -0.1200 2.1500 0.0 -0.01 1.9 ! ethylene glycol, xhe +CD325A 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! CPEN, cyclopentane, viv +CD325B 0.0 -0.0600 2.0200 0.0 -0.01 1.9 ! THF, tetrahydrofuran, from CPEN, viv +CD326A 0.0 -0.0560 2.1000 0.0 -0.01 1.9 ! CHEX, from CD32A, 9/09, cmb +CD326B 0.0 -0.0560 2.0100 0.0 -0.01 1.9 ! THP, tetrahydropyran, viv +CD33A 0.0 -0.0780 2.0400 0.0 -0.01 1.9 ! ETHA, ethane, 4/98, yin, adm jr. +CD33B 0.0 -0.1100 2.0400 0.0 -0.01 1.9 ! special methyl C for MEOH, methanol +CD33C 0.0 -0.0780 1.9400 ! special methyl C for amides +!CD33D 0.0 -0.0780 1.9400 ! special methyl C for MAS, CT1, lipid conflict +CD33E 0.0 -0.1040 2.0000 0.0 -0.01 1.9 ! DMEE, ethers, cmb 11/08 + +!! Nitrogens +ND2A1 0.0 -0.1600 1.8500 ! ACEM, acetamide +ND2A2 0.0 -0.2000 1.8300 ! NMA, N-methylacetamide +ND2A3 0.0 -0.2500 1.9600 ! DMA +ND2B1 0.0 -0.1850 1.6590 ! NA bases, jal +ND2R5A 0.0 -0.0870 1.8610 ! IMID, imidazole (N-H donor) +ND2R5B 0.0 -0.0690 1.9560 ! IMID, imidazole (N acceptor) +ND2R5C 0.0 -0.1050 1.8500 ! IMIM, imidazolium, EH, fylin 2018 +ND2R5D 0.0 -0.2770 1.9950 ! N9 in ADE, jal +ND2R5E 0.0 -0.0980 1.7480 ! NA bases, jal +ND2R5F 0.0 -0.2770 1.9950 ! N9 in GUA, jal +ND2R6A 0.0 -0.0650 1.9800 ! PYR, pyridine (N acceptor) +ND2R6B 0.0 -0.1340 1.9140 ! PYRM, pyrimidine (N acceptor), jal +ND2R6C 0.0 -0.1180 1.8440 ! GUAB, guanine (N donor), jal +ND2R6D 0.0 -0.1180 1.8440 ! N1 in THY, jal +ND2P1A 0.0 -0.0950 1.8000 ! MGUAN/GUAN, fylin, mar27, 2018 +ND3P2A 0.0 -0.3600 1.3800 ! protonated sp3 N, NC2/NC3/NC4, fylin, mar27, 2018 +ND3P3A 0.0 -0.0250 1.5500 ! protonated sp3 N, NC1/NH4, fylin, mar27, 2018 +ND3A2 0.0 -0.3680 1.9000 ! mam1, eam1, pam1, fylin 2018 +ND3A3 0.0 -0.2000 1.8000 ! imino N + +!! Oxygens +OD2C1A 0.0 -0.2000 1.7800 ! NMA, N-methylacetamide (ACEM) +OD2C1B 0.0 -0.2030 1.7740 ! NA bases carbonyl O, jal +OD2C1C 0.0 -0.1750 1.8750 ! aldehydes +OD2C1D 0.0 -0.2000 1.8500 ! ketones/aldehydes +OD2C2A 0.0 -0.3000 1.8200 ! ACET, fylin, mar27, 2018 +OD2C2B 0.0 -0.1900 1.8650 ! DMP, cmb, lipids & nucleic acids +OD2C3A 0.0 -0.1800 1.7500 ! from OD2C3B for lipids L JC-v2-24 +OD30A 0.0 -0.0600 1.7400 ! ether, +OD30B 0.0 -0.1700 1.7700 ! DMP, cmb, 06/09, lipids, merge with NA phosphate post 2017 +OD30BR 0.0 -0.1700 1.7700 ! DMP, nucleic acids, copied for RNA, jal, reset to OD30B, alex +OD30C 0.0 -0.1220 1.7500 ! from OD30CL for lipids: MAS/ACEH series OD30C and OD30D is the only different parameter +OD30D 0.0 -0.1720 1.7100 ! ester O in terminal phosphates +OD30E 0.0 -0.8300 1.5200 ! PHET, fylin, mar27, 2018 +OD305A 0.0 -0.0800 1.7200 ! THF, tetrahydrofuran, drude+lp,H2O int.+ cond phase 11/18/08 cmb +OD306A 0.0 -0.0800 1.7400 ! THP, tetrahydropyran, drude+lp,H2O int.+ cond phase 11/18/08 cmb +OD31A 0.0 -0.1500 1.7650 ! alcohols, va +OD31B 0.0 -0.1500 1.7400 ! alcohols, va, long chain primary alcohols +OD31C 0.0 -0.2500 1.5500 ! Phenol, p-Cresol +OD31D 0.0 -0.1500 1.7650 ! methylphosphate hydroxyl O +OD31E 0.0 -0.2000 1.7000 ! ethylene glycol +OD31F 0.0 -0.1720 1.7100 ! protonated hydroxyl in an acid (ACEH) +OD31G 0.0 -0.1500 1.7650 ! alcohol on nucleic acid 3'terminal sugar (DNA/RNA 3TER) +ODW 0.0 -0.21094325 1.78692899 ! SWM4, SWM4-NDP water, GL, 2005 +ODW6 0.0 -0.1620 1.7950 ! SWM6-NDP water +! Sulfurs +SD1A 0.0 -0.2700 1.9000 ! sulfate ion, based on PD1A, a&a +SD31A 0.0 -0.4300 2.0500 ! MESH +SD31B 0.0 -0.4200 2.0200 ! ETSH, PRSH +SD30A 0.0 -0.3100 2.0500 ! EMS +SD30B 0.0 -0.3200 2.0000 ! DMDS +SD2C2A 0.0 -0.2000 2.1700 ! MES, thiolates +SD2C2B 0.0 -0.1000 2.2600 ! ETS +! Phosphorous +PD1A 0.0 -0.2700 1.9000 ! DMP, lipids +! Halogens +! halogenated ethanes +FDA1 0.0 -0.1750 1.6200 ! FETH, DFET +FDA3 0.0 -0.0800 1.6200 ! TFET +CLDA1 0.0 -0.3600 1.9400 ! CLET, DCLE +CLDA3 0.0 -0.2700 1.9300 ! TCLE +BRDA1 0.0 -0.4600 2.0300 ! BRET, DBRE, TBRE +IDA1 0.0 -0.5600 2.2000 ! IETH, DIET, TIET +! halogenated benzenes +FDR1 0.0 -0.1100 1.6500 ! FLUB +CLDR1 0.0 -0.2900 1.9400 ! CHLB +BRDR1 0.0 -0.4000 2.0400 ! BROB +IDR1 0.0 -0.5700 2.1800 ! IODB +!! Monovalent Ions +!Yu et al., JCTC, 6, 774-786, 2010 +LID 0.0 -0.03000 1.1000000 ! Li +SODD 0.0 -0.03151 1.4616800 ! Na +POTD 0.0 -0.1419265 1.6866521 ! K +RBD 0.0 -0.2730669 1.7855083 ! Rb +CSD 0.0 -0.2766036 2.0238218 ! Cs +FAD 0.0 -0.0026181 2.4622406 ! Flouride +CLAD 0.0 -0.0719737 2.4811139 ! Cloride +BRAD 0.0 -0.0823440 2.6262883 ! Bromide +IAD 0.0 -0.2084343 2.7579694 ! Iodide +!! Divalent Ions +! Requires the use of NB Thole parameters +! Yu et al. JCTC 6, 774-786, 2010 +BAD 0.0 -0.6000 1.5717385 ! Ba +CALD 0.0 -0.2100 1.2708552 ! Ca +MAGD 0.0 -0.0500 1.1264156 ! Mg +SRD 0.0 -0.3400 1.3059400 ! Sr +ZND 0.0 -0.2500 0.9349678 ! Zn + +! Lone pairs +LPA1 0.0 -0.0000 0.0100 ! cation-pi lonepair, fylin +LPA2 0.0 -0.0000 0.0100 ! cation-pi lonepair, fylin +LPA3 0.0 -0.0000 0.0100 ! cation-pi lonepair, fylin +LP5N 0.0 -0.0000 0.0100 ! cation-pi lonepair, fylin + +LPD 0.0 -0.0000 0.0100 ! General Lone pair; no NBFIX terms +LPDW 0.0 -0.0000 0.0100 ! Lone pairs on water: Note overlap of SWM4 and SWM6 LPs +LPDO1 0.0 -0.0000 0.0100 ! Lone pairs on OD2C1A in NMA, peptide bond +LPDNA1 0.0 -0.0000 0.0100 ! General Nucleic Acid Lone pairs +LPR 0.0 -0.1000 2.0500 ! Repulsive LP, for sulfates, XZ +! Drudes, do not use D* wildcard +! small radii added to allow compatability with OpenMM +DRUD 0.0 -0.0000 0.0100 ! Generic Drudes +DOH2 0.0 -0.0000 0.0100 ! water Drude +DF2 0.0 -0.0000 0.0100 ! F Drude, flub +DCL2 0.0 -0.0000 0.0100 ! CL Drude for benzenes +DCL3 0.0 -0.0000 0.0100 ! CL Drude for ethane +DBR2 0.0 -0.0000 0.0100 ! BR Drude +DI2 0.0 -0.0000 0.0100 ! I Drude +!! Rare gas parameters +DUM 0.0 -0.0000 0.0100 ! dummy atom +XED 0.0 -0.02127 1.4800 ! HE, helium, experimental pot. energy surface, adm jr., 12/95 +NED 0.0 -0.0860 1.5300 ! NE, neon, semiempirical pot. energy surface, adm jr., 12/95 +!Do NOT put atom type with all zero values as the last LJ parameter due to a bug in CHARMM + +NBFIX +! In column 1 place the water or ion (positive before negative) atom type +! For non water/ion terms place in alphabetical order +ODW CD2O3A -0.11528 3.48690 ! MAS, PEML +ODW CD2R6B -0.14080 3.85690 ! PYR, pyridine, PEML +ODW CD2R6C -0.15090 3.83690 ! PYRM, pyrimidine, PEML +ODW ND2A2 -0.20540 3.63690 ! NMA, PEML +ODW ND3A2 -0.36000 3.48200 ! neutral aliphatic amines, MAM1, EAM1, PAM1, dGwat, fylin 2018 +ODW ND2R6B -0.22589 3.85792 ! acceptor nitrogen in purines and pyrimidines, jal +ODW OD2C1A -0.20540 3.60690 ! NMA, PEML +ODW OD2C1B -0.20540 3.68690 ! THY, CYT, URA, GUA, jal +ODW OD2C3A -0.27942 3.62321 ! ester carbonyl O for lipids +ODW OD30C -0.16583 3.53691 ! ester sp3 O for lipids +ODW OD305A -0.14990 3.54690 ! THF, 01/12 xhe +ODW OD306A -0.14990 3.58690 ! THP, 01/12 xhe +ODW SD30A -0.26572 3.82693 ! EMS, Xiao +ODW SD30B -0.26981 3.78693 ! DMDS, Xiao + +! Ions +LID CLAD -0.04647 3.80000 ! chloride, Savelyev-2015 +LID ND2B1 -0.06928 3.60000 ! primary amine, nucleic acid bases, Savelyev-2015 +LID ND2R6B -0.05477 3.60000 ! acceptor nitrogen in purines and pyrimidines, nucleic acids, Savelyev-2015 +LID ND2R6C -0.06123 3.60000 ! acceptor nitrogen nucleic acids pyrimidines, Savelyev-2015 +LID OD2C2B -0.04582 3.13500 ! phosphate anionic O, lipids & nucleic acids, Savelyev-2015 +LID OD30B -0.02449 3.02000 ! phosphate ester O, lipids & nucleic acids, Savelyev-2015 +LID OD30BR -0.02449 3.02000 ! phosphate ester O, nucleic acids, Savelyev-2015, RNA specific + +!! NOTE (2/11/2019): NBFIX and NBTHOLE from Hui-2015 should be considered +!! experimental as they may lead to ion over-binding. These terms will be +!! subject to systematic refinement in the near future (MacKerell, Noskov, Lemkul). +SODD CLAD -0.04762 4.09000 ! chloride, Savelyev-2014 +SODD LPDO1 -0.06000 2.77000 ! protein backbone/amide, Hui-2015 +SODD ND2B1 -0.07100 3.78000 ! primary amine, nucleic acid bases, Savelyev-2015 +SODD ND2R6B -0.05600 3.79000 ! acceptor nitrogen in purines and pyrimidines, Savelyev-2014 +SODD ND2R6C -0.06276 3.62000 ! acceptor nitrogen nucleic acids pyrimidines, Savelyev-2014 +SODD OD2C1A -0.09000 2.88000 ! protein backbone/amide, Hui-2015 +SODD OD2C2A -0.07939 3.47000 ! glu, asp, Noskov, 2018 +SODD OD2C2B -0.04696 3.49668 ! phosphate anionic O, lipids & nucleic acids, Savelyev-2014 +SODD OD30B -0.02510 3.38168 ! phosphate ester O, lipids & nucleic acids, Savelyev-2014 +SODD OD30BR -0.02510 3.38168 ! phosphate ester O, nucleic acids, Savelyev-2014, RNA specific +SODD OD30D -0.02510 3.38168 ! phosphate ester O, MP_1 +SODD OD31A -0.06000 3.07000 ! ethanol, ser, thr, Hui-2015 +SODD OD31B -0.06000 3.07000 ! from SODD OD31A +SODD OD31C -0.06000 3.07000 ! from SODD OD31A +SODD OD31E -0.06000 3.07000 ! from SODD OD31A +SODD OD31F -0.06000 3.07000 ! from SODD OD31A +SODD OD31G -0.06000 3.07000 ! from SODD OD31A + +POTD CLAD -0.10107 4.21000 ! Savelyev-2015 +POTD LPDO1 -0.07000 3.02000 ! protein backbone/amide, Hui-2015 +POTD ND2B1 -0.15060 3.80000 ! primary amine, nucleic acid bases, Savelyev-2015 +POTD ND2R6B -0.11913 3.80000 ! acceptor nitrogen in purines and pyrimidines, Savelyev-2015 +POTD ND2R6C -0.13319 3.70000 ! acceptor nitrogen nucleic acids pyrimidines, Savelyev-2015 +POTD OD2C1A -0.18000 3.21000 ! protein backbone/amide, Hui-2015 +! original NBFIX from Hui Li JPCB 2015 leads to ion over-binding +! reparametrized by jal by tuning to ACET..K+ QM interaction energy +! and validated in osmotic pressure calculations +POTD OD2C2A -0.16850 3.75000 ! glu, asp, jal 2018, from osmotic pressure +POTD OD31A -0.15000 3.34000 ! ethanol, ser, thr, Hui-2015 +POTD OD31B -0.15000 3.34000 ! from POTD OD31A +POTD OD31C -0.15000 3.34000 ! from POTD OD31A +POTD OD31E -0.15000 3.34000 ! from POTD OD31A +POTD OD31F -0.15000 3.34000 ! from POTD OD31A +POTD OD31G -0.15000 3.34000 ! from POTD OD31A + +RBD CLAD -0.14019 4.27000 ! Savelyev-2015 +RBD ND2B1 -0.20902 3.80000 ! primary amine, nucleic acid bases, Savelyev-2015 +RBD ND2R6B -0.16524 3.82000 ! acceptor nitrogen in purines and pyrimidines, Savelyev-2015 +RBD ND2R6C -0.18475 3.70000 ! acceptor nitrogen nucleic acids pyrimidines, Savelyev-2015 + +MAGD DOH2 -0.07500 2.65500 ! damp water dipole, improves dissociation kinetics, jal +MAGD LPDO1 -0.14500 2.36100 ! protein backbone/amide LPDO1 on OD2C1A +MAGD ND2R6B -0.09031 3.13208 ! Cyt-N3, Ade-N3/N1, Gua-N3, jal +MAGD ND2R5E -0.16925 2.68762 ! Ade/Gua-N7 +MAGD ND2R6C -0.06991 3.37008 ! Cyt-N1, Thy-N3, Ura-N1/N3, Gua-N1 +MAGD ND2R6D -0.06991 3.37008 ! Thy-N1 +MAGD ND2B1 -0.10818 3.10817 ! Cyt-N4, Ade-N6, Gua-N2 +MAGD OD2C1A -0.10050 2.72900 ! protein backbone/amide LPDO1 on OD2C1A +MAGD OD2C1B -0.28833 2.43438 ! Cyt-O2, Thy-O2/O4, Ura-O2/O4, Gua-O6 +MAGD OD2C2B -0.31211 2.59990 ! phosphate anionic O, lipids & nucleic acids +MAGD OD30B -0.40592 4.40157 ! phosphate ester O, lipids & nucleic acids +MAGD OD30BR -0.40592 4.40157 ! phosphate ester O, nucleic acids, RNA specific +MAGD OD30D -0.40592 2.25157 ! phosphate ester O, MP_1 + +! calcium +!CALD LPDO1 -0.37000 2.50000 ! protein backbone/amide, Hui-2015, commented until testing complete +!CALD OD2C1A -0.22000 2.85000 ! protein backbone/amide, Hui-2015, commented until testing complete +!CALD OD2C2A -0.11000 3.51500 ! glu, asp, Hui-2015, commented until testing complete +!CALD OD31A -0.10000 3.28000 ! ethanol, ser, thr, Hui-2015, commented until testing complete +!CALD OD31B -0.10000 3.28000 ! from CALD OD31A, commented until testing complete +!CALD OD31C -0.10000 3.28000 ! from CALD OD31A, commented until testing complete +!CALD OD31E -0.10000 3.28000 ! from CALD OD31A, commented until testing complete +!CALD OD31F -0.10000 3.28000 ! from CALD OD31A, commented until testing complete +!CALD OD31G -0.10000 3.28000 ! from CALD OD31A, commented until testing complete + +! chloride +CLAD HDP1A -0.00100 3.54000 ! protein/backbone, Hui-2015, undergoing testing +CLAD ND2A2 -0.08000 4.65000 ! protein/backbone, Hui-2015, undergoing testing +CLAD ND2B1 -0.07000 4.31000 ! nucleic acids, Savelyev-2014 +CLAD ND2R5D -0.07000 4.31000 ! nucleic acids, Savelyev-2014 +CLAD ND2R5E -0.07000 4.31000 ! nucleic acids, Savelyev-2014 +CLAD ND2R5F -0.07000 4.31000 ! nucleic acids, Savelyev-2014 +CLAD ND2R6B -0.07000 4.31000 ! nucleic acids, Savelyev-2014 +CLAD ND2R6C -0.07000 4.31000 ! nucleic acids, Savelyev-2014 +CLAD ND2R6D -0.07000 4.31000 ! nucleic acids, Savelyev-2014 +CLAD OD31A -0.10390 4.05000 ! ethanol, ser, thr, Hui-2015, undergoing testing +CLAD OD31B -0.10390 4.05000 ! from CLAD OD31B, undergoing testing +CLAD OD31C -0.10390 4.05000 ! from CLAD OD31B, undergoing testing +CLAD OD31E -0.10390 4.05000 ! from CLAD OD31B, undergoing testing +CLAD OD31F -0.10390 4.05000 ! from CLAD OD31B, undergoing testing +CLAD OD31G -0.10390 4.05000 ! from CLAD OD31B, undergoing testing + +!lone pair - acceptor, Savelyev-2014 and 2015 +LPDNA1 LID -0.09000 2.60000 ! nucleic acid bases +LPDNA1 SODD -0.09000 2.92000 ! nucleic acid bases +LPDNA1 POTD -0.09000 3.37000 ! nucleic acid bases +LPDNA1 RBD -0.09000 3.57000 ! nucleic acid bases +LPDNA1 MAGD -0.16504 2.20163 ! nucleic acid bases + +! Halogens, fyl +! halogens and water oxygen +ODW FDA1 -0.18900 3.57000 ! FETH, DFET +ODW FDA3 -0.05000 3.93000 ! TFET +ODW CLDA1 -0.25000 3.56000 ! CLET, DCLE +ODW CLDA3 -0.19800 3.60000 ! TCLE +ODW BRDA1 -0.26200 3.63000 ! BRET/DBRE/TBRE +ODW IDA1 -0.24500 3.96000 ! IETH/DIET/TIET +ODW FDR1 -0.14000 3.58000 ! FLUB +ODW CLDR1 -0.14500 3.60000 ! CLET +ODW BRDR1 -0.17800 3.78000 ! BROB +ODW IDR1 -0.24500 3.96000 ! IODB +! halogen drude and water hydrogen +HDW DF2 -0.00800 2.87000 ! FLUB +HDW DCL2 -0.04100 3.00000 ! CHLB +HDW DCL3 -0.04000 2.97000 ! CLET, DCLE, TCLE +HDW DBR2 -0.07000 3.07000 ! BROB/BRET/DBRE/TBRE +HDW DI2 -0.10000 3.24000 ! IODB/IETH/DIET/TIET + +! Halogen NBFIXes with protein and other macromolecule residues +! DCL2/DCL3 with HDP1A for all neutral hydrogen bond donors +!================================================== +DCL2 HDP1A -0.01900 3.01800 ! CHLB's HBD-H +DCL3 HDP1A -0.04000 2.87000 ! CLET/DCLE/TCLE's HBD-H +DBR2 HDP1A -0.08000 3.03500 ! BROB's HBD-H + +! chlorobenzene based +!---------------------------------------------------------- +CLDR1 ND2A1 -0.20000 3.85000 ! CHLB..ACEM +DCL2 ND2A1 -0.10000 3.85000 ! CHLB..ACEM +CLDR1 ND2A2 -0.18000 3.87000 ! CHLB..NMA +DCL2 ND2A2 -0.10000 3.69000 ! CHLB..NMA +CLDR1 ND2B1 -0.20000 3.85000 ! from CLDR1 ND2A1, ACEM (with na) +DCL2 ND2B1 -0.10000 3.85000 ! from DCL2 ND2A1, ACEM (with na) +CLDR1 ND2R5A -0.26000 3.70000 ! CHLB..IMID +DCL2 ND2R5A -0.06600 3.70000 ! CHLB..IMID +CLDR1 ND2R5B -0.12500 3.68000 ! CHLB..IMID +DCL2 ND2R5B -0.05000 3.68000 ! CHLB..IMID +CLDR1 ND2R5E -0.12500 3.68000 ! from CLDR1 ND2R5B, IMID (with na) +DCL2 ND2R5E -0.05000 3.68000 ! from DCL2 ND2R5B, IMID (with na) +CLDR1 ND2R6A -0.12500 3.68000 ! from CLDR1 ND2R5B, IMID, alex, for pyridine (with na) +DCL2 ND2R6A -0.05000 3.68000 ! from DCL2 ND2R5B, IMID, alex, for pyridine (with na) +CLDR1 ND2R6B -0.12500 3.68000 ! from CLDR1 ND2R5B, IMID (with na) +DCL2 ND2R6B -0.05000 3.68000 ! from DCL2 ND2R5B, IMID (with na) +CLDR1 ND2R6C -0.18000 3.87000 ! from CLDR1 ND2A2, NMA, alex (with na) +DCL2 ND2R6C -0.10000 3.69000 ! from DCL2 ND2A2, NMA, alex (with na) +CLDR1 ND2P1A -0.28000 3.78000 ! CHLB..MGUAN (DCL2/DCL3..HDP1B unnecessary) +CLDR1 ND3P3A -0.26000 3.76000 ! CHLB..NC1 (DCL2/DCL3..HDP1B unnecessary) +CLDR1 OD2C1A -0.30000 3.32000 ! CHLB..NMA +DCL2 OD2C1A -0.10000 3.32000 ! CHLB..NMA +CLDR1 OD2C1B -0.30000 3.32000 ! from CLDR1 OD2C1A, NMA (with na) +DCL2 OD2C1B -0.10000 3.32000 ! from DCL2 OD2C1A, NMA (with na) +CLDR1 OD2C1C -0.30000 3.32000 ! from CLDR1 OD2C1A, NMA (with carb.) +DCL2 OD2C1C -0.10000 3.32000 ! from DCL2 OD2C1A, NMA (with carb.) +CLDR1 OD2C1D -0.30000 3.32000 ! from CLDR1 OD2C1A, NMA (with carb.) +DCL2 OD2C1D -0.10000 3.32000 ! from DCL2 OD2C1A, NMA (with carb.) +CLDR1 OD2C2A -0.13500 3.49000 ! CHLB..ACET +DCL2 OD2C2A -0.13000 3.49000 ! CHLB..ACET +CLDR1 OD2C2B -0.13500 3.49000 ! from CLDR1 OD2C2A, ACET, alex, for phosphate (with lipids & na) +DCL2 OD2C2B -0.13000 3.49000 ! from DCL2 OD2C2A, ACET, alex (with lipids & na) +CLDR1 OD2C3A -0.30000 3.32000 ! from CLDR1 OD2C1A, NMA, alex, ester (with lipids) +DCL2 OD2C3A -0.10000 3.32000 ! from DCL2 OD2C1A, NMA, alex (with lipids) +CLDR1 OD31A -0.06000 3.56000 ! CHLB..MEOH +DCL2 OD31A -0.10500 3.56000 ! CHLB..MEOH +CLDR1 OD31B -0.06000 3.56000 ! CHLB..MEOH +DCL2 OD31B -0.10500 3.56000 ! CHLB..MEOH +CLDR1 OD31C -0.13700 3.49000 ! CHLB..PHEN +DCL2 OD31C -0.11200 3.49000 ! CHLB..PHEN +CLDR1 OD31E -0.06000 3.56000 ! from CLDR1 OD31A, MEOH (with carb.) +DCL2 OD31E -0.10500 3.56000 ! from DCL2 OD31A, MEOH (with carb.) +CLDR1 OD31F -0.06000 3.56000 ! CHLB..MEOH, alex, for OH in neutral acid +DCL2 OD31F -0.10500 3.56000 ! CHLB..MEOH, alex +CLDR1 OD31G -0.06000 3.56000 ! from CLDR1 OD31A, MEOH, alex (with na) +DCL2 OD31G -0.10500 3.56000 ! from DCL2 OD31A, MEOH, alex (with na) +CLDR1 SD31A -0.23000 3.81000 ! CHLB..MESH +DCL2 SD31A -0.30000 3.81000 ! CHLB..MESH +CLDR1 SD31B -0.23000 3.81000 ! CHLB..MESH, alex, for ETSH, CYS +DCL2 SD31B -0.30000 3.81000 ! CHLB..MESH, alex + +! mono, di and trichloroethane based +!---------------------------------------------------------- +CLDA1 ND2A1 -0.30000 3.70000 ! CLET/DCET..ACEM +CLDA3 ND2A1 -0.10000 3.86000 ! TCLE..ACEM +DCL3 ND2A1 -0.10000 3.70000 ! CLET/DCET..ACEM +CLDA1 ND2A2 -0.35000 3.55000 ! TCLE..NMA +CLDA3 ND2A2 -0.45000 3.58000 ! TCLE..NMA +DCL3 ND2A2 -0.10000 3.68000 ! CLET/DCLE/TCLE..NMA +CLDA1 ND2B1 -0.30000 3.70000 ! from CLDA1 ND2A1, ACEM (with na) +CLDA3 ND2B1 -0.10000 3.86000 ! from CLDA3 ND2A1, ACEM (with na) +DCL3 ND2B1 -0.10000 3.70000 ! from DCL3 ND2A1, ACEM (with na) +CLDA1 ND2R5A -0.13000 3.75000 ! CLET/DCLE..IMID +CLDA3 ND2R5A -0.18500 3.92000 ! TCLE..IMID +DCL3 ND2R5A -0.05600 3.85000 ! TCLE..IMID +CLDA1 ND2R5B -0.12500 3.68000 ! CLET/DCLE..IMID +CLDA3 ND2R5B -0.02000 3.93000 ! TCLE..IMID +DCL3 ND2R5B -0.05000 3.90000 ! CLET/DCLE/TCLE..IMID +CLDA1 ND2R5E -0.12500 3.68000 ! from CLDA1 ND2R5B, IMID (with na) +CLDA3 ND2R5E -0.02000 3.93000 ! from CLDA3 ND2R5B, IMID (with na) +DCL3 ND2R5E -0.05000 3.90000 ! from DCL3 ND2R5B, IMID (with na) +CLDA1 ND2R6A -0.12500 3.68000 ! from CLDA1 ND2R5B, IMID, alex, for pyridine (with na) +CLDA3 ND2R6A -0.02000 3.93000 ! from CLDA3 ND2R5B, IMID, alex, for pyridine (with na) +DCL3 ND2R6A -0.05000 3.90000 ! from DCL3 ND2R5B, IMID, alex, for pyridine (with na) +CLDA1 ND2R6B -0.12500 3.68000 ! from CLDA1 ND2R5B, IMID (with na) +CLDA3 ND2R6B -0.02000 3.93000 ! from CLDA3 ND2R5B, IMID (with na) +DCL3 ND2R6B -0.05000 3.90000 ! from DCL3 ND2R5B, IMID (with na) +CLDA1 ND2R6C -0.35000 3.55000 ! from CLDA1 ND2A2, NMA (with na) +CLDA3 ND2R6C -0.45000 3.58000 ! from CLDA3 ND2A2, NMA (with na) +DCL3 ND2R6C -0.10000 3.68000 ! from DCL3 ND2A2, NMA (with na) +CLDA1 ND2P1A -0.28000 3.78000 ! CLET..MGUAN (DCL2/DCL3..HDP1B unnecessary) +CLDA1 ND3P3A -0.13000 3.73000 ! CLET..NC1 (DCL2/DCL3..HDP1B unnecessary) +CLDA1 OD2C1A -0.30000 3.10000 ! CLET/DCLE..NMA +CLDA3 OD2C1A -0.10000 3.26000 ! TCLE..NMA +DCL3 OD2C1A -0.25000 3.48000 ! CLET/DCLE/TCLE..NMA +CLDA1 OD2C2A -0.13500 3.49000 ! CLET/DCLE..ACET +DCL3 OD2C2A -0.13000 3.49000 ! CLET/DCLE..ACET +CLDA1 OD2C1B -0.30000 3.10000 ! from CLDA1 OD2C1A, NMA (with na) +CLDA3 OD2C1B -0.10000 3.26000 ! from CLDA3 OD2C1A, NMA (with na) +DCL3 OD2C1B -0.25000 3.48000 ! from DCL3 OD2C1A, NMA (with na) +CLDA1 OD2C1C -0.30000 3.10000 ! from CLDA1 OD2C1A, NMA (with carb.) +CLDA3 OD2C1C -0.10000 3.26000 ! from CLDA3 OD2C1A, NMA (with carb.) +DCL3 OD2C1C -0.25000 3.48000 ! from DCL3 OD2C1A, NMA (with carb.) +CLDA1 OD2C1D -0.30000 3.10000 ! from CLDA1 OD2C1A, NMA (with carb.) +CLDA3 OD2C1D -0.10000 3.26000 ! from CLDA3 OD2C1A, NMA (with carb.) +DCL3 OD2C1D -0.25000 3.48000 ! from DCL3 OD2C1A, NMA (with carb.) +CLDA1 OD2C2B -0.13500 3.49000 ! from CLDA1 OD2C2A, ACET 4check (with lipids & na) +DCL3 OD2C2B -0.13000 3.49000 ! from DCL3 OD2C2A, ACET, alex (with lipids & na) +CLDA1 OD2C3A -0.30000 3.10000 ! from CLDA1 OD2C1A, NMA 4check (with lipids) +CLDA3 OD2C3A -0.10000 3.26000 ! from CLDA3 OD2C1A, NMA 4check (with lipids) +DCL3 OD2C3A -0.25000 3.48000 ! from DCL3 OD2C1A, NMA 4check (with lipids) +CLDA1 OD31A -0.05000 3.73000 ! CLET/DCLE..MEOH +CLDA3 OD31A -0.03500 3.85000 ! TCLE..MEOH +DCL3 OD31A -0.09000 3.59000 ! CLET/DCLE/TCLE..MEOH +CLDA1 OD31B -0.05000 3.73000 ! CLET/DCLE..MEOH +CLDA3 OD31B -0.03500 3.85000 ! TCLE..MEOH +DCL3 OD31B -0.09000 3.59000 ! CLET/DCLE/TCLE..MEOH +CLDA1 OD31C -0.01000 3.61000 ! CLET/DCLE..PHEN +CLDA3 OD31C -0.06000 3.67000 ! TCLE..PHEN +DCL3 OD31C -0.07500 3.65000 ! CLET/DCLE/TCLE..PHEN +CLDA1 OD31E -0.05000 3.73000 ! from CLDA1 OD31A, MEOH (with carb.) +CLDA3 OD31E -0.03500 3.85000 ! from CLDA3 OD31A, MEOH (with carb.) +DCL3 OD31E -0.09000 3.59000 ! from DCL3 OD31A, MEOH (with carb.) +CLDA1 OD31F -0.05000 3.73000 ! CLET/DCLE..MEOH, alex, for OH in neutral acid +CLDA3 OD31F -0.03500 3.85000 ! TCLE..MEOH, alex +DCL3 OD31F -0.09000 3.59000 ! CLET/DCLE/TCLE..MEOH, alex +CLDA1 OD31G -0.05000 3.73000 ! from CLDA1 OD31A, MEOH (with na) +CLDA3 OD31G -0.03500 3.85000 ! from CLDA3 OD31A, MEOH (with na) +DCL3 OD31G -0.09000 3.59000 ! from DCL3 OD31A, MEOH (with na) +CLDA1 SD31A -0.18000 3.93000 ! CLET/DCLE..MESH +CLDA3 SD31A -0.13000 3.90000 ! TCLE..MESH +DCL3 SD31A -0.20000 3.99000 ! CLET/DCLE/TCLE..MESH +CLDA1 SD31B -0.18000 3.93000 ! CLET/DCLE..MESH, alex, for ETSH +CLDA3 SD31B -0.13000 3.90000 ! TCLE..MESH, alex +DCL3 SD31B -0.20000 3.99000 ! CLET/DCLE/TCLE..MESH, alex + +! bromobenzene based +BRDR1 ND2A1 -0.30000 3.82000 ! BROB..ACEM +DBR2 ND2A1 -0.10000 3.82000 ! BROB..ACEM +BRDR1 ND2A2 -0.26000 3.78000 ! BROB..NMA +DBR2 ND2A2 -0.13000 3.78000 ! BROB..NMA +BRDR1 ND2B1 -0.30000 3.82000 ! from BRDR1 ND2A1, ACEM (with na) +DBR2 ND2B1 -0.10000 3.82000 ! from DBR2 ND2A1, ACEM (with na) +BRDR1 ND2R5A -0.60000 3.37000 ! BROB..IMID/INDO +DBR2 ND2R5A -0.20000 3.37000 ! BROB..IMID/INDO +BRDR1 ND2R5B -0.20000 3.76000 ! BROB..IMID +DBR2 ND2R5B -0.05000 3.76000 ! BROB..IMID +BRDR1 ND2R5E -0.20000 3.76000 ! from BRDR1 ND2R5B, IMID (with na) +DBR2 ND2R5E -0.05000 3.76000 ! from DBR2 ND2R5B, IMID (with na) +BRDR1 ND2R6A -0.20000 3.76000 ! from BRDR1 ND2R5B, IMID, alex, for pyridine (with na) +DBR2 ND2R6A -0.05000 3.76000 ! from DBR2 ND2R5B, IMID, alex, for pyridine (with na) +BRDR1 ND2R6B -0.20000 3.76000 ! from BRDR1 ND2R5B, IMID (with na) +DBR2 ND2R6B -0.05000 3.76000 ! from DBR2 ND2R5B, IMID (with na) +BRDR1 ND2R6C -0.26000 3.78000 ! from BRDR1 ND2A2, NMA, alex (with na) +DBR2 ND2R6C -0.13000 3.78000 ! from DBR2 ND2A2, NMA, alex (with na) +BRDR1 ND2P1A -0.68000 3.73000 ! BROB..MGUAN (DBR2..HDP1B is not necessary) +BRDR1 ND3P3A -0.95500 3.50000 ! BROB..NC1 (DBR2..HDP1B is not necessary) +BRDR1 OD2C1A -0.13000 3.70000 ! BROB..NMA +DBR2 OD2C1A -0.10000 3.70000 ! BROB..NMA +BRDR1 OD2C1B -0.13000 3.70000 ! from BRDR1 OD2C1A, NMA (with na) +DBR2 OD2C1B -0.10000 3.70000 ! from DBR2 OD2C1A, NMA (with na) +BRDR1 OD2C1C -0.13000 3.70000 ! from BRDR1 OD2C1A, NMA (with carb.) +DBR2 OD2C1C -0.10000 3.70000 ! from DBR2 OD2C1A, NMA (with carb.) +BRDR1 OD2C1D -0.30000 3.32000 ! from BRDR1 OD2C1A, NMA (with carb.) +DBR2 OD2C1D -0.10000 3.32000 ! from DBR2 OD2C1A, NMA (with carb.) +BRDR1 OD2C2A -0.09500 4.10000 ! BROB..ACET +DBR2 OD2C2A -0.01500 3.85000 ! BROB..ACET +BRDR1 OD2C2B -0.09500 4.10000 ! from BRDR1 OD2C2A, ACET, alex (with lipids & na) +DBR2 OD2C2B -0.01500 3.85000 ! from DBR2 OD2C2A, ACET, alex (with lipids & na) +BRDR1 OD2C3A -0.13000 3.70000 ! from BRDR1 OD2C1A, NMA, alex (with lipids) +DBR2 OD2C3A -0.10000 3.70000 ! from DBR2 OD2C1A, NMA, alex (with lipids) +BRDR1 OD31A -0.19000 3.56000 ! BROB..MEOH +DBR2 OD31A -0.19000 3.56000 ! BROB..MEOH +BRDR1 OD31B -0.19000 3.56000 ! BROB..MEOH +DBR2 OD31B -0.19000 3.56000 ! BROB..MEOH +BRDR1 OD31E -0.19000 3.56000 ! from BRDR1 OD31A, MEOH (with carb.) +DBR2 OD31E -0.19000 3.56000 ! from DBR2 OD31A, MEOH (with carb.) +BRDR1 OD31F -0.19000 3.56000 ! from BRDR1 OD31A, MEOH, alex, for OH in neutral acid +DBR2 OD31F -0.19000 3.56000 ! from BR2 OD31A, MEOH, alex +BRDR1 OD31G -0.19000 3.56000 ! from BRDR1 OD31A, MEOH, alex (with na) +DBR2 OD31G -0.19000 3.56000 ! from DBR2 OD31A, MEOH, alex (with na) +BRDR1 SD31A -0.35000 3.72000 ! BROB..MESH +DBR2 SD31A -0.25000 3.72000 ! BROB..MESH +BRDR1 SD31B -0.35000 3.72000 ! BROB..MESH, alex, for ETSH, CYS +DBR2 SD31B -0.25000 3.72000 ! BROB..MESH, alex + +! nucleic acid specific, jal: to disfavor 5'-syn state of Ade/Gua +OD31A ND2R6B -0.04762 4.13429 + +! phen/cres-oh...nc1 +OD31C ND3P3A -0.010 4.05 ! to prevent it being too favorable, fylin 11/2018 + +! fylin - protein charged protein interaction, 2018 +! ========================================= +!NC1/MGUAN..acetNC1/MGUAN..acetNC1/MGUAN..acet +HDP1B OD2C2A -0.015 2.58 ! +ND3P3A OD2C2A -0.058 3.85 ! fylin add at 12/04/2018 + +! MGUAN-N..acet +ND2P1A OD2C2A -0.013 4.12 ! +CD2N1A OD2C2A -0.085 3.62 ! fylin, 12/2018 + +! IMIM..acet +ND2R5C OD2C2A -0.037 3.82 ! +CD2R5D OD2C2A -0.013 3.90 ! +CD2R5E OD2C2A -0.013 3.90 ! + + +! NBFIX for Cation/Anion-Pi interaction - 2019 +! ========================================== +! BENZ/TOLU/CRES/PHEN/INDO/MIND...NC1 +! ------------------------------------------ +CD2R6A ND3P3A -0.020 3.85 ! +CD2R6D ND3P3A -0.090 3.85 ! +LPA1 ND3P3A -0.080 3.85 ! +LPA2 ND3P3A -0.005 3.85 ! +LPA3 ND3P3A -0.040 3.85 ! + +! BENZ/TOLU/CRES/PHEN/INDO/MIND...MGUAN +! ------------------------------------------ +CD2R6A ND2P1A -0.300 3.90 ! +CD2R6D ND2P1A -0.400 3.80 ! +LPA1 CD2N1A -0.050 3.80 ! +LPA2 ND2P1A -0.850 4.00 ! +LPA3 CD2N1A -0.850 3.85 ! + +! BENZ/TOLU/CRES/PHEN/INDO/MIND...IMIM +! ------------------------------------------ +CD2R6A ND2R5C -0.530 3.80 ! +CD2R6D ND2R5C -0.100 3.90 ! +LPA1 ND2R5C -0.200 4.00 ! +LPA2 ND2R5C -0.890 3.20 ! + +! BENZ/TOLU/CRES/PHEN/INDO/MIND...ACET +! ------------------------------------------ +CD2R6A OD2C2A -0.600 3.65 ! +LPA1 OD2C2A -0.050 3.60 ! +LPA2 OD2C2A -0.680 4.10 ! +LPA3 OD2C2A -0.200 3.65 ! +CD2R6D OD2C2A -0.100 3.65 ! + +! IMID/4MIM/4MIE..NC1 ! +! ------------------------------------------ +CD2R5A ND3P3A -0.010 3.60 ! +CD2R5B ND3P3A -0.010 4.25 ! +ND2R5A ND3P3A -0.100 3.80 ! +ND2R5B ND3P3A -0.010 3.70 ! +LP5N ND3P3A -0.200 3.80 ! + +! IMID/4MIM/4MIE..MGUAN ! +! ------------------------------------------ +CD2R5A ND2P1A -0.250 3.90 ! +CD2R5B ND2P1A -0.720 3.88 ! +ND2R5A ND2P1A -0.080 3.95 ! +ND2R5B ND2P1A -0.044 3.90 ! +LP5N CD2N1A -0.400 4.00 ! + +! IMID/4MIM/4MIE..IMIM +! ------------------------------------------ +CD2R5A ND2R5C -0.600 3.65 ! +CD2R5B ND2R5C -0.100 4.05 ! +ND2R5A ND2R5C -0.450 3.90 ! +ND2R5B ND2R5C -0.100 3.95 ! +LP5N ND2R5C -0.300 3.95 ! +ND2R5B CD2R5E -0.300 3.95 ! + +! INDO/MIND/4MIM/4MIE ..ACET +! ------------------------------------------ +CD2R5B OD2C2A -0.885 3.60 ! +ND2R5B OD2C2A -0.885 3.60 ! +! ----------------------------------------- +! INDO/MIND/4MIM/4MIE/IMID-ND2R5A..ACET +CD2R5A OD2C2A -0.020 3.80 ! +ND2R5A OD2C2A -0.055 3.80 ! + +!===== End of NBFIX for Cation-Pi ========= + +THOLE TCUT 5.0 MAXNBTHOLE 5000 +!command for NAMD is "drudeNbtholeCut 5" + +! Lipid Opt - Yalun, 2022 +OD2C2B CD32B 1.45000 + +ODW BAD 1.45869 +ODW CALD 1.50877 +ODW MAGD 1.51567 +ODW SRD 1.23792 +ODW ZND 2.14773 + +SODD OD2C1A 1.04000 ! protein backbone/amide, Hui-2015, undergoing testing +SODD OD2C2A 0.43000 ! protein, glu, asp, Hui-2015, undergoing testing +SODD OD31A 1.82000 ! ethanol, ser, thr, Hui-2015, undergoing testing +SODD OD31B 1.82000 ! from SODD OD31A, undergoing testing +SODD OD31C 1.82000 ! from SODD OD31A, undergoing testing +SODD OD31E 1.82000 ! from SODD OD31A, undergoing testing +SODD OD31F 1.82000 ! from SODD OD31A, undergoing testing +SODD OD31G 1.82000 ! from SODD OD31A, undergoing testing + +POTD OD2C1A 2.19000 ! protein backbone/amide, Hui-2015, undergoing testing +! previous NBTHOLE from Hui Li JPCB 2015 leads to ion over-binding +! reparametrized by jal by tuning to ACET..K+ QM interaction energy +! and validated in osmotic pressure calculations +POTD OD2C2A 0.75000 ! jal 2018, from osmotic pressure + +MAGD CLAD 0.66000 ! chloride, nucleic acids, jal +MAGD ND2A2 1.49100 ! Cyt-N1, Thy-N3, Ura-N1/N3, Gua-N1, from MAGD ND2R6C for amide, secondary (NMA, peptide bond) +MAGD ND2B1 1.34300 ! Cyt-N4, Ade-N6, Gua-N2, jal +MAGD ND2R5B 1.38400 ! Ade/Gua-N7, neutral his unprotonated ring nitrogen +MAGD ND2R5E 1.38400 ! Ade/Gua-N7 +MAGD ND2R6A 1.17300 ! Cyt-N3, Ade-N3/N1, Gua-N3, aromatic N, 6-membered ring (pyridine) +MAGD ND2R6B 1.17300 ! Cyt-N3, Ade-N3/N1, Gua-N3 +MAGD ND2R6C 1.49100 ! Cyt-N1, Thy-N3, Ura-N1/N3, Gua-N1 +MAGD ND2R6D 1.49100 ! Thy-N1 +MAGD OD2C1A 1.07600 ! protein backbone/amide LPDO1 on OD2C1A +MAGD OD2C1B 1.10900 ! Cyt-O2, Thy-O2/O4, Ura-O2/O4, Gua-O6 +MAGD OD2C2B 1.44900 ! lipids and nucleic acids, phosphate anionic +MAGD OD30B 1.15100 ! lipids and nucleic acids, phosphate ester O +MAGD OD30BR 1.15100 ! nucleic acids, phosphate ester O, RNA specific +MAGD OD30D 1.15100 ! nucleic acids, phosphate ester O, methylphosphates +MAGD OD31D 1.95000 ! based on methylphosphate hydroxyl, transfer to other hydroxyls requires testing + +! calcium +!CALD OD2C1A 1.32000 ! protein backbone/amide, Hui-2015, commented until testing complete +!CALD OD2C1B 1.32000 ! protein backbone/amide, Hui-2015, for Cyt-O2, Thy-O2/O4, Ura-O2/O4, Gua-O6, +!CALD OD31A 1.05000 ! ethanol, ser, thr, Hui-2015, commented until testing complete +!CALD OD31B 1.05000 ! from CALD OD31A, commented until testing complete +!CALD OD31C 1.05000 ! from CALD OD31A, commented until testing complete +!CALD OD31E 1.05000 ! from CALD OD31A, commented until testing complete +!CALD OD31F 1.05000 ! from CALD OD31A, commented until testing complete +!CALD OD31G 1.05000 ! from CALD OD31A, commented until testing complete + +BAD OD2C1A 1.20000 ! NMA protein backbone (from ion-NMA interaction) + +ZND OD2C1A 1.50000 ! NMA protein backbone (from ion-NMA interaction) + +! chloride +CLAD ND2A2 2.86000 ! protein backbone/amide, Hui-2015, undergoing testing +CLAD ND2R6C 2.86000 ! protein backbone/amide, Hui-2015, for Cyt-N1, Thy-N3, Ura-N1/N3, Gua-N1, undergoing testing + +! nucleic acid specific +CD32C OD2C2B 1.45000 !-1.642 -0.931 !phosphate anionic O to C5' special 1,4 term + +END + diff --git a/versioneer.py b/versioneer.py index 64fea1c8..1e3753e6 100644 --- a/versioneer.py +++ b/versioneer.py @@ -1,5 +1,5 @@ -# Version: 0.18 +# Version: 0.29 """The Versioneer - like a rocketeer, but for versions. @@ -7,18 +7,14 @@ ============== * like a rocketeer, but for versions! -* https://github.com/warner/python-versioneer +* https://github.com/python-versioneer/python-versioneer * Brian Warner -* License: Public Domain -* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy -* [![Latest Version] -(https://pypip.in/version/versioneer/badge.svg?style=flat) -](https://pypi.python.org/pypi/versioneer/) -* [![Build Status] -(https://travis-ci.org/warner/python-versioneer.png?branch=master) -](https://travis-ci.org/warner/python-versioneer) - -This is a tool for managing a recorded version number in distutils-based +* License: Public Domain (Unlicense) +* Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3 +* [![Latest Version][pypi-image]][pypi-url] +* [![Build Status][travis-image]][travis-url] + +This is a tool for managing a recorded version number in setuptools-based python projects. The goal is to remove the tedious and error-prone "update the embedded version string" step from your release process. Making a new release should be as easy as recording a new tag in your version-control @@ -27,9 +23,38 @@ ## Quick Install -* `pip install versioneer` to somewhere to your $PATH -* add a `[versioneer]` section to your setup.cfg (see below) -* run `versioneer install` in your source tree, commit the results +Versioneer provides two installation modes. The "classic" vendored mode installs +a copy of versioneer into your repository. The experimental build-time dependency mode +is intended to allow you to skip this step and simplify the process of upgrading. + +### Vendored mode + +* `pip install versioneer` to somewhere in your $PATH + * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is + available, so you can also use `conda install -c conda-forge versioneer` +* add a `[tool.versioneer]` section to your `pyproject.toml` or a + `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) + * Note that you will need to add `tomli; python_version < "3.11"` to your + build-time dependencies if you use `pyproject.toml` +* run `versioneer install --vendor` in your source tree, commit the results +* verify version information with `python setup.py version` + +### Build-time dependency mode + +* `pip install versioneer` to somewhere in your $PATH + * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is + available, so you can also use `conda install -c conda-forge versioneer` +* add a `[tool.versioneer]` section to your `pyproject.toml` or a + `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md)) +* add `versioneer` (with `[toml]` extra, if configuring in `pyproject.toml`) + to the `requires` key of the `build-system` table in `pyproject.toml`: + ```toml + [build-system] + requires = ["setuptools", "versioneer[toml]"] + build-backend = "setuptools.build_meta" + ``` +* run `versioneer install --no-vendor` in your source tree, commit the results +* verify version information with `python setup.py version` ## Version Identifiers @@ -61,7 +86,7 @@ for example `git describe --tags --dirty --always` reports things like "0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the 0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes. +uncommitted changes). The version identifier is used for multiple purposes: @@ -166,7 +191,7 @@ Some situations are known to cause problems for Versioneer. This details the most significant ones. More can be found on Github -[issues page](https://github.com/warner/python-versioneer/issues). +[issues page](https://github.com/python-versioneer/python-versioneer/issues). ### Subprojects @@ -180,7 +205,7 @@ `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI distributions (and upload multiple independently-installable tarballs). * Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other langauges) in subdirectories. + provide bindings to Python (and perhaps other languages) in subdirectories. Versioneer will look for `.git` in parent directories, and most operations should get the right version string. However `pip` and `setuptools` have bugs @@ -194,9 +219,9 @@ Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in some later version. -[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking +[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking this issue. The discussion in -[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the +[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the issue from the Versioneer side in more detail. [pip PR#3176](https://github.com/pypa/pip/pull/3176) and [pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve @@ -224,31 +249,20 @@ cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into a different virtualenv), so this can be surprising. -[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes +[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes this one, but upgrading to a newer version of setuptools should probably resolve it. -### Unicode version strings - -While Versioneer works (and is continually tested) with both Python 2 and -Python 3, it is not entirely consistent with bytes-vs-unicode distinctions. -Newer releases probably generate unicode version strings on py2. It's not -clear that this is wrong, but it may be surprising for applications when then -write these strings to a network connection or include them in bytes-oriented -APIs like cryptographic checksums. - -[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates -this question. - ## Updating Versioneer To upgrade your project to a new release of Versioneer, do the following: * install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg`, if necessary, to include any new configuration settings - indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install` in your source tree, to replace +* edit `setup.cfg` and `pyproject.toml`, if necessary, + to include any new configuration settings indicated by the release notes. + See [UPGRADING](./UPGRADING.md) for details. +* re-run `versioneer install --[no-]vendor` in your source tree, to replace `SRC/_version.py` * commit any changed files @@ -265,35 +279,70 @@ direction and include code from all supported VCS systems, reducing the number of intermediate scripts. +## Similar projects + +* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time + dependency +* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of + versioneer +* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools + plugin ## License To make Versioneer easier to embed, all its code is dedicated to the public domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . +Specifically, both are released under the "Unlicense", as described in +https://unlicense.org/. + +[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg +[pypi-url]: https://pypi.python.org/pypi/versioneer/ +[travis-image]: +https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg +[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer """ +# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring +# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements +# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error +# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with +# pylint:disable=attribute-defined-outside-init,too-many-arguments -from __future__ import print_function -try: - import configparser -except ImportError: - import ConfigParser as configparser +import configparser import errno import json import os import re import subprocess import sys +from pathlib import Path +from typing import Any, Callable, cast, Dict, List, Optional, Tuple, Union +from typing import NoReturn +import functools + +have_tomllib = True +if sys.version_info >= (3, 11): + import tomllib +else: + try: + import tomli as tomllib + except ImportError: + have_tomllib = False class VersioneerConfig: """Container for Versioneer configuration parameters.""" + VCS: str + style: str + tag_prefix: str + versionfile_source: str + versionfile_build: Optional[str] + parentdir_prefix: Optional[str] + verbose: Optional[bool] + -def get_root(): +def get_root() -> str: """Get the project root directory. We require that all commands are run from the project root, i.e. the @@ -301,13 +350,23 @@ def get_root(): """ root = os.path.realpath(os.path.abspath(os.getcwd())) setup_py = os.path.join(root, "setup.py") + pyproject_toml = os.path.join(root, "pyproject.toml") versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): + if not ( + os.path.exists(setup_py) + or os.path.exists(pyproject_toml) + or os.path.exists(versioneer_py) + ): # allow 'python path/to/setup.py COMMAND' root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) setup_py = os.path.join(root, "setup.py") + pyproject_toml = os.path.join(root, "pyproject.toml") versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): + if not ( + os.path.exists(setup_py) + or os.path.exists(pyproject_toml) + or os.path.exists(versioneer_py) + ): err = ("Versioneer was unable to run the project root directory. " "Versioneer requires setup.py to be executed from " "its immediate directory (like 'python setup.py COMMAND'), " @@ -321,43 +380,62 @@ def get_root(): # module-import table will cache the first one. So we can't use # os.path.dirname(__file__), as that will find whichever # versioneer.py was first imported, even in later projects. - me = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(me)[0]) + my_path = os.path.realpath(os.path.abspath(__file__)) + me_dir = os.path.normcase(os.path.splitext(my_path)[0]) vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir: + if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals(): print("Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py)) + % (os.path.dirname(my_path), versioneer_py)) except NameError: pass return root -def get_config_from_root(root): +def get_config_from_root(root: str) -> VersioneerConfig: """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise EnvironmentError (if setup.cfg is missing), or + # This might raise OSError (if setup.cfg is missing), or # configparser.NoSectionError (if it lacks a [versioneer] section), or # configparser.NoOptionError (if it lacks "VCS="). See the docstring at # the top of versioneer.py for instructions on writing your setup.cfg . - setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.SafeConfigParser() - with open(setup_cfg, "r") as f: - parser.readfp(f) - VCS = parser.get("versioneer", "VCS") # mandatory - - def get(parser, name): - if parser.has_option("versioneer", name): - return parser.get("versioneer", name) - return None + root_pth = Path(root) + pyproject_toml = root_pth / "pyproject.toml" + setup_cfg = root_pth / "setup.cfg" + section: Union[Dict[str, Any], configparser.SectionProxy, None] = None + if pyproject_toml.exists() and have_tomllib: + try: + with open(pyproject_toml, 'rb') as fobj: + pp = tomllib.load(fobj) + section = pp['tool']['versioneer'] + except (tomllib.TOMLDecodeError, KeyError) as e: + print(f"Failed to load config from {pyproject_toml}: {e}") + print("Try to load it from setup.cfg") + if not section: + parser = configparser.ConfigParser() + with open(setup_cfg) as cfg_file: + parser.read_file(cfg_file) + parser.get("versioneer", "VCS") # raise error if missing + + section = parser["versioneer"] + + # `cast`` really shouldn't be used, but its simplest for the + # common VersioneerConfig users at the moment. We verify against + # `None` values elsewhere where it matters + cfg = VersioneerConfig() - cfg.VCS = VCS - cfg.style = get(parser, "style") or "" - cfg.versionfile_source = get(parser, "versionfile_source") - cfg.versionfile_build = get(parser, "versionfile_build") - cfg.tag_prefix = get(parser, "tag_prefix") - if cfg.tag_prefix in ("''", '""'): + cfg.VCS = section['VCS'] + cfg.style = section.get("style", "") + cfg.versionfile_source = cast(str, section.get("versionfile_source")) + cfg.versionfile_build = section.get("versionfile_build") + cfg.tag_prefix = cast(str, section.get("tag_prefix")) + if cfg.tag_prefix in ("''", '""', None): cfg.tag_prefix = "" - cfg.parentdir_prefix = get(parser, "parentdir_prefix") - cfg.verbose = get(parser, "verbose") + cfg.parentdir_prefix = section.get("parentdir_prefix") + if isinstance(section, configparser.SectionProxy): + # Make sure configparser translates to bool + cfg.verbose = section.getboolean("verbose") + else: + cfg.verbose = section.get("verbose") + return cfg @@ -366,37 +444,48 @@ class NotThisMethod(Exception): # these dictionaries contain VCS-specific tools -LONG_VERSION_PY = {} -HANDLERS = {} +LONG_VERSION_PY: Dict[str, str] = {} +HANDLERS: Dict[str, Dict[str, Callable]] = {} -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): +def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator + """Create decorator to mark a method as the handler of a VCS.""" + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f + HANDLERS.setdefault(vcs, {})[method] = f return f return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): +def run_command( + commands: List[str], + args: List[str], + cwd: Optional[str] = None, + verbose: bool = False, + hide_stderr: bool = False, + env: Optional[Dict[str, str]] = None, +) -> Tuple[Optional[str], Optional[int]]: """Call the given command(s).""" assert isinstance(commands, list) - p = None - for c in commands: + process = None + + popen_kwargs: Dict[str, Any] = {} + if sys.platform == "win32": + # This hides the console window if pythonw.exe is used + startupinfo = subprocess.STARTUPINFO() + startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW + popen_kwargs["startupinfo"] = startupinfo + + for command in commands: try: - dispcmd = str([c] + args) + dispcmd = str([command] + args) # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) + process = subprocess.Popen([command] + args, cwd=cwd, env=env, + stdout=subprocess.PIPE, + stderr=(subprocess.PIPE if hide_stderr + else None), **popen_kwargs) break - except EnvironmentError: - e = sys.exc_info()[1] + except OSError as e: if e.errno == errno.ENOENT: continue if verbose: @@ -407,26 +496,25 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, if verbose: print("unable to find command, tried %s" % (commands,)) return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: + stdout = process.communicate()[0].strip().decode() + if process.returncode != 0: if verbose: print("unable to run %s (error)" % dispcmd) print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode + return None, process.returncode + return stdout, process.returncode -LONG_VERSION_PY['git'] = ''' +LONG_VERSION_PY['git'] = r''' # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build # directories (produced by setup.py build) will contain a much shorter file # that just contains the computed version number. -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) +# This file is released into the public domain. +# Generated by versioneer-0.29 +# https://github.com/python-versioneer/python-versioneer """Git implementation of _version.py.""" @@ -435,9 +523,11 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, import re import subprocess import sys +from typing import Any, Callable, Dict, List, Optional, Tuple +import functools -def get_keywords(): +def get_keywords() -> Dict[str, str]: """Get the keywords needed to look up the version information.""" # these strings will be replaced by git during git-archive. # setup.py/versioneer.py will grep for the variable names, so they must @@ -453,8 +543,15 @@ def get_keywords(): class VersioneerConfig: """Container for Versioneer configuration parameters.""" + VCS: str + style: str + tag_prefix: str + parentdir_prefix: str + versionfile_source: str + verbose: bool + -def get_config(): +def get_config() -> VersioneerConfig: """Create, populate and return the VersioneerConfig() object.""" # these strings are filled in when 'setup.py versioneer' creates # _version.py @@ -472,13 +569,13 @@ class NotThisMethod(Exception): """Exception raised if a method is not valid for the current scenario.""" -LONG_VERSION_PY = {} -HANDLERS = {} +LONG_VERSION_PY: Dict[str, str] = {} +HANDLERS: Dict[str, Dict[str, Callable]] = {} -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): +def register_vcs_handler(vcs: str, method: str) -> Callable: # decorator + """Create decorator to mark a method as the handler of a VCS.""" + def decorate(f: Callable) -> Callable: """Store f in HANDLERS[vcs][method].""" if vcs not in HANDLERS: HANDLERS[vcs] = {} @@ -487,22 +584,35 @@ def decorate(f): return decorate -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): +def run_command( + commands: List[str], + args: List[str], + cwd: Optional[str] = None, + verbose: bool = False, + hide_stderr: bool = False, + env: Optional[Dict[str, str]] = None, +) -> Tuple[Optional[str], Optional[int]]: """Call the given command(s).""" assert isinstance(commands, list) - p = None - for c in commands: + process = None + + popen_kwargs: Dict[str, Any] = {} + if sys.platform == "win32": + # This hides the console window if pythonw.exe is used + startupinfo = subprocess.STARTUPINFO() + startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW + popen_kwargs["startupinfo"] = startupinfo + + for command in commands: try: - dispcmd = str([c] + args) + dispcmd = str([command] + args) # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) + process = subprocess.Popen([command] + args, cwd=cwd, env=env, + stdout=subprocess.PIPE, + stderr=(subprocess.PIPE if hide_stderr + else None), **popen_kwargs) break - except EnvironmentError: - e = sys.exc_info()[1] + except OSError as e: if e.errno == errno.ENOENT: continue if verbose: @@ -513,18 +623,20 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, if verbose: print("unable to find command, tried %%s" %% (commands,)) return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: + stdout = process.communicate()[0].strip().decode() + if process.returncode != 0: if verbose: print("unable to run %%s (error)" %% dispcmd) print("stdout was %%s" %% stdout) - return None, p.returncode - return stdout, p.returncode + return None, process.returncode + return stdout, process.returncode -def versions_from_parentdir(parentdir_prefix, root, verbose): +def versions_from_parentdir( + parentdir_prefix: str, + root: str, + verbose: bool, +) -> Dict[str, Any]: """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both @@ -533,15 +645,14 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): """ rootdirs = [] - for i in range(3): + for _ in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return {"version": dirname[len(parentdir_prefix):], "full-revisionid": None, "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level + rootdirs.append(root) + root = os.path.dirname(root) # up a level if verbose: print("Tried directories %%s but none started with prefix %%s" %% @@ -550,41 +661,48 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): @register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): +def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. - keywords = {} + keywords: Dict[str, str] = {} try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: + with open(versionfile_abs, "r") as fobj: + for line in fobj: + if line.strip().startswith("git_refnames ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["refnames"] = mo.group(1) + if line.strip().startswith("git_full ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["full"] = mo.group(1) + if line.strip().startswith("git_date ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["date"] = mo.group(1) + except OSError: pass return keywords @register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): +def git_versions_from_keywords( + keywords: Dict[str, str], + tag_prefix: str, + verbose: bool, +) -> Dict[str, Any]: """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") + if "refnames" not in keywords: + raise NotThisMethod("Short version file found") date = keywords.get("date") if date is not None: + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] + # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 # -like" string, which we must then edit to make compliant), because @@ -597,11 +715,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) + refs = {r.strip() for r in refnames.strip("()").split(",")} # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) + tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %%d @@ -610,7 +728,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) + tags = {r for r in refs if re.search(r'\d', r)} if verbose: print("discarding '%%s', no digits" %% ",".join(refs - tags)) if verbose: @@ -619,6 +737,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): r = ref[len(tag_prefix):] + # Filter out refs that exactly match prefix or that don't start + # with a number once the prefix is stripped (mostly a concern + # when prefix is '') + if not re.match(r'\d', r): + continue if verbose: print("picking %%s" %% r) return {"version": r, @@ -634,7 +757,12 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): @register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): +def git_pieces_from_vcs( + tag_prefix: str, + root: str, + verbose: bool, + runner: Callable = run_command +) -> Dict[str, Any]: """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* @@ -645,8 +773,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) + # GIT_DIR can interfere with correct operation of Versioneer. + # It may be intended to be passed to the Versioneer-versioned project, + # but that should not change where we get our version from. + env = os.environ.copy() + env.pop("GIT_DIR", None) + runner = functools.partial(runner, env=env) + + _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, + hide_stderr=not verbose) if rc != 0: if verbose: print("Directory %%s not under git control" %% root) @@ -654,24 +789,57 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%%s*" %% tag_prefix], - cwd=root) + describe_out, rc = runner(GITS, [ + "describe", "--tags", "--dirty", "--always", "--long", + "--match", f"{tag_prefix}[[:digit:]]*" + ], cwd=root) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) + full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) if full_out is None: raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() - pieces = {} + pieces: Dict[str, Any] = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None + branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], + cwd=root) + # --abbrev-ref was added in git-1.6.3 + if rc != 0 or branch_name is None: + raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") + branch_name = branch_name.strip() + + if branch_name == "HEAD": + # If we aren't exactly on a branch, pick a branch which represents + # the current commit. If all else fails, we are on a branchless + # commit. + branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) + # --contains was added in git-1.5.4 + if rc != 0 or branches is None: + raise NotThisMethod("'git branch --contains' returned error") + branches = branches.split("\n") + + # Remove the first line if we're running detached + if "(" in branches[0]: + branches.pop(0) + + # Strip off the leading "* " from the list of branches. + branches = [branch[2:] for branch in branches] + if "master" in branches: + branch_name = "master" + elif not branches: + branch_name = None + else: + # Pick the first branch that is returned. Good or bad. + branch_name = branches[0] + + pieces["branch"] = branch_name + # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] # TAG might have hyphens. git_describe = describe_out @@ -688,7 +856,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # TAG-NUM-gHEX mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) if not mo: - # unparseable. Maybe git-describe is misbehaving? + # unparsable. Maybe git-describe is misbehaving? pieces["error"] = ("unable to parse git-describe output: '%%s'" %% describe_out) return pieces @@ -713,26 +881,27 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits + out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) + pieces["distance"] = len(out.split()) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"], - cwd=root)[0].strip() + date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip() + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces -def plus_or_dot(pieces): +def plus_or_dot(pieces: Dict[str, Any]) -> str: """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" -def render_pep440(pieces): +def render_pep440(pieces: Dict[str, Any]) -> str: """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you @@ -757,23 +926,71 @@ def render_pep440(pieces): return rendered -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. +def render_pep440_branch(pieces: Dict[str, Any]) -> str: + """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . + + The ".dev0" means not master branch. Note that .dev0 sorts backwards + (a feature branch will appear "older" than the master branch). Exceptions: - 1: no tags. 0.post.devDISTANCE + 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0" + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+untagged.%%d.g%%s" %% (pieces["distance"], + pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: + """Split pep440 version string at the post-release segment. + + Returns the release segments before the post-release and the + post-release version number (or -1 if no post-release segment is present). + """ + vc = str.split(ver, ".post") + return vc[0], int(vc[1] or 0) if len(vc) == 2 else None + + +def render_pep440_pre(pieces: Dict[str, Any]) -> str: + """TAG[.postN.devDISTANCE] -- No -dirty. + + Exceptions: + 1: no tags. 0.post0.devDISTANCE + """ + if pieces["closest-tag"]: if pieces["distance"]: - rendered += ".post.dev%%d" %% pieces["distance"] + # update the post release segment + tag_version, post_version = pep440_split_post(pieces["closest-tag"]) + rendered = tag_version + if post_version is not None: + rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"]) + else: + rendered += ".post0.dev%%d" %% (pieces["distance"]) + else: + # no commits, use the tag as the version + rendered = pieces["closest-tag"] else: # exception #1 - rendered = "0.post.dev%%d" %% pieces["distance"] + rendered = "0.post0.dev%%d" %% pieces["distance"] return rendered -def render_pep440_post(pieces): +def render_pep440_post(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards @@ -800,12 +1017,41 @@ def render_pep440_post(pieces): return rendered -def render_pep440_old(pieces): +def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: + """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . + + The ".dev0" means not master branch. + + Exceptions: + 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += ".post%%d" %% pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "g%%s" %% pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0.post%%d" %% pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+g%%s" %% pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def render_pep440_old(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. - Eexceptions: + Exceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: @@ -822,7 +1068,7 @@ def render_pep440_old(pieces): return rendered -def render_git_describe(pieces): +def render_git_describe(pieces: Dict[str, Any]) -> str: """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. @@ -842,7 +1088,7 @@ def render_git_describe(pieces): return rendered -def render_git_describe_long(pieces): +def render_git_describe_long(pieces: Dict[str, Any]) -> str: """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. @@ -862,7 +1108,7 @@ def render_git_describe_long(pieces): return rendered -def render(pieces, style): +def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: return {"version": "unknown", @@ -876,10 +1122,14 @@ def render(pieces, style): if style == "pep440": rendered = render_pep440(pieces) + elif style == "pep440-branch": + rendered = render_pep440_branch(pieces) elif style == "pep440-pre": rendered = render_pep440_pre(pieces) elif style == "pep440-post": rendered = render_pep440_post(pieces) + elif style == "pep440-post-branch": + rendered = render_pep440_post_branch(pieces) elif style == "pep440-old": rendered = render_pep440_old(pieces) elif style == "git-describe": @@ -894,7 +1144,7 @@ def render(pieces, style): "date": pieces.get("date")} -def get_versions(): +def get_versions() -> Dict[str, Any]: """Get version information or return default if unable to do so.""" # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have # __file__, we can work backwards from there to the root. Some @@ -915,7 +1165,7 @@ def get_versions(): # versionfile_source is the relative path from the top of the source # tree (where the .git directory might live) to this file. Invert # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): + for _ in cfg.versionfile_source.split('/'): root = os.path.dirname(root) except NameError: return {"version": "0+unknown", "full-revisionid": None, @@ -942,41 +1192,48 @@ def get_versions(): @register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): +def git_get_keywords(versionfile_abs: str) -> Dict[str, str]: """Extract version information from the given file.""" # the code embedded in _version.py can just fetch the value of these # keywords. When used from setup.py, we don't want to import _version.py, # so we do it with a regexp instead. This function is not used from # _version.py. - keywords = {} + keywords: Dict[str, str] = {} try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: + with open(versionfile_abs, "r") as fobj: + for line in fobj: + if line.strip().startswith("git_refnames ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["refnames"] = mo.group(1) + if line.strip().startswith("git_full ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["full"] = mo.group(1) + if line.strip().startswith("git_date ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["date"] = mo.group(1) + except OSError: pass return keywords @register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): +def git_versions_from_keywords( + keywords: Dict[str, str], + tag_prefix: str, + verbose: bool, +) -> Dict[str, Any]: """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") + if "refnames" not in keywords: + raise NotThisMethod("Short version file found") date = keywords.get("date") if date is not None: + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] + # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 # -like" string, which we must then edit to make compliant), because @@ -989,11 +1246,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) + refs = {r.strip() for r in refnames.strip("()").split(",")} # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) + tags = {r[len(TAG):] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -1002,7 +1259,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) + tags = {r for r in refs if re.search(r'\d', r)} if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -1011,6 +1268,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # sorting will prefer e.g. "2.0" over "2.0rc1" if ref.startswith(tag_prefix): r = ref[len(tag_prefix):] + # Filter out refs that exactly match prefix or that don't start + # with a number once the prefix is stripped (mostly a concern + # when prefix is '') + if not re.match(r'\d', r): + continue if verbose: print("picking %s" % r) return {"version": r, @@ -1026,7 +1288,12 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): @register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): +def git_pieces_from_vcs( + tag_prefix: str, + root: str, + verbose: bool, + runner: Callable = run_command +) -> Dict[str, Any]: """Get version from 'git describe' in the root of the source tree. This only gets called if the git-archive 'subst' keywords were *not* @@ -1037,8 +1304,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) + # GIT_DIR can interfere with correct operation of Versioneer. + # It may be intended to be passed to the Versioneer-versioned project, + # but that should not change where we get our version from. + env = os.environ.copy() + env.pop("GIT_DIR", None) + runner = functools.partial(runner, env=env) + + _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root, + hide_stderr=not verbose) if rc != 0: if verbose: print("Directory %s not under git control" % root) @@ -1046,24 +1320,57 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) + describe_out, rc = runner(GITS, [ + "describe", "--tags", "--dirty", "--always", "--long", + "--match", f"{tag_prefix}[[:digit:]]*" + ], cwd=root) # --long was added in git-1.5.5 if describe_out is None: raise NotThisMethod("'git describe' failed") describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) + full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root) if full_out is None: raise NotThisMethod("'git rev-parse' failed") full_out = full_out.strip() - pieces = {} + pieces: Dict[str, Any] = {} pieces["long"] = full_out pieces["short"] = full_out[:7] # maybe improved later pieces["error"] = None + branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"], + cwd=root) + # --abbrev-ref was added in git-1.6.3 + if rc != 0 or branch_name is None: + raise NotThisMethod("'git rev-parse --abbrev-ref' returned error") + branch_name = branch_name.strip() + + if branch_name == "HEAD": + # If we aren't exactly on a branch, pick a branch which represents + # the current commit. If all else fails, we are on a branchless + # commit. + branches, rc = runner(GITS, ["branch", "--contains"], cwd=root) + # --contains was added in git-1.5.4 + if rc != 0 or branches is None: + raise NotThisMethod("'git branch --contains' returned error") + branches = branches.split("\n") + + # Remove the first line if we're running detached + if "(" in branches[0]: + branches.pop(0) + + # Strip off the leading "* " from the list of branches. + branches = [branch[2:] for branch in branches] + if "master" in branches: + branch_name = "master" + elif not branches: + branch_name = None + else: + # Pick the first branch that is returned. Good or bad. + branch_name = branches[0] + + pieces["branch"] = branch_name + # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] # TAG might have hyphens. git_describe = describe_out @@ -1080,7 +1387,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): # TAG-NUM-gHEX mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) if not mo: - # unparseable. Maybe git-describe is misbehaving? + # unparsable. Maybe git-describe is misbehaving? pieces["error"] = ("unable to parse git-describe output: '%s'" % describe_out) return pieces @@ -1105,19 +1412,20 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): else: # HEX: no tags pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits + out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root) + pieces["distance"] = len(out.split()) # total number of commits # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() + date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() + # Use only the last line. Previous lines may contain GPG signature + # information. + date = date.splitlines()[-1] pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) return pieces -def do_vcs_install(manifest_in, versionfile_source, ipy): +def do_vcs_install(versionfile_source: str, ipy: Optional[str]) -> None: """Git-specific installation logic for Versioneer. For Git, this means creating/changing .gitattributes to mark _version.py @@ -1126,36 +1434,40 @@ def do_vcs_install(manifest_in, versionfile_source, ipy): GITS = ["git"] if sys.platform == "win32": GITS = ["git.cmd", "git.exe"] - files = [manifest_in, versionfile_source] + files = [versionfile_source] if ipy: files.append(ipy) - try: - me = __file__ - if me.endswith(".pyc") or me.endswith(".pyo"): - me = os.path.splitext(me)[0] + ".py" - versioneer_file = os.path.relpath(me) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) + if "VERSIONEER_PEP518" not in globals(): + try: + my_path = __file__ + if my_path.endswith((".pyc", ".pyo")): + my_path = os.path.splitext(my_path)[0] + ".py" + versioneer_file = os.path.relpath(my_path) + except NameError: + versioneer_file = "versioneer.py" + files.append(versioneer_file) present = False try: - f = open(".gitattributes", "r") - for line in f.readlines(): - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - f.close() - except EnvironmentError: + with open(".gitattributes", "r") as fobj: + for line in fobj: + if line.strip().startswith(versionfile_source): + if "export-subst" in line.strip().split()[1:]: + present = True + break + except OSError: pass if not present: - f = open(".gitattributes", "a+") - f.write("%s export-subst\n" % versionfile_source) - f.close() + with open(".gitattributes", "a+") as fobj: + fobj.write(f"{versionfile_source} export-subst\n") files.append(".gitattributes") run_command(GITS, ["add", "--"] + files) -def versions_from_parentdir(parentdir_prefix, root, verbose): +def versions_from_parentdir( + parentdir_prefix: str, + root: str, + verbose: bool, +) -> Dict[str, Any]: """Try to determine the version from the parent directory name. Source tarballs conventionally unpack into a directory that includes both @@ -1164,15 +1476,14 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): """ rootdirs = [] - for i in range(3): + for _ in range(3): dirname = os.path.basename(root) if dirname.startswith(parentdir_prefix): return {"version": dirname[len(parentdir_prefix):], "full-revisionid": None, "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level + rootdirs.append(root) + root = os.path.dirname(root) # up a level if verbose: print("Tried directories %s but none started with prefix %s" % @@ -1181,7 +1492,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose): SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.18) from +# This file was generated by 'versioneer.py' (0.29) from # revision-control system data, or from the parent directory name of an # unpacked source archive. Distribution tarballs contain a pre-generated copy # of this file. @@ -1198,12 +1509,12 @@ def get_versions(): """ -def versions_from_file(filename): +def versions_from_file(filename: str) -> Dict[str, Any]: """Try to determine the version from _version.py if present.""" try: with open(filename) as f: contents = f.read() - except EnvironmentError: + except OSError: raise NotThisMethod("unable to read _version.py") mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S) @@ -1215,9 +1526,8 @@ def versions_from_file(filename): return json.loads(mo.group(1)) -def write_to_version_file(filename, versions): +def write_to_version_file(filename: str, versions: Dict[str, Any]) -> None: """Write the given version number to the given _version.py file.""" - os.unlink(filename) contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) with open(filename, "w") as f: @@ -1226,14 +1536,14 @@ def write_to_version_file(filename, versions): print("set %s to '%s'" % (filename, versions["version"])) -def plus_or_dot(pieces): +def plus_or_dot(pieces: Dict[str, Any]) -> str: """Return a + if we don't already have one, else return a .""" if "+" in pieces.get("closest-tag", ""): return "." return "+" -def render_pep440(pieces): +def render_pep440(pieces: Dict[str, Any]) -> str: """Build up version string, with post-release "local version identifier". Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you @@ -1258,23 +1568,71 @@ def render_pep440(pieces): return rendered -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. +def render_pep440_branch(pieces: Dict[str, Any]) -> str: + """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] . + + The ".dev0" means not master branch. Note that .dev0 sorts backwards + (a feature branch will appear "older" than the master branch). Exceptions: - 1: no tags. 0.post.devDISTANCE + 1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty] """ if pieces["closest-tag"]: rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0" + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+untagged.%d.g%s" % (pieces["distance"], + pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]: + """Split pep440 version string at the post-release segment. + + Returns the release segments before the post-release and the + post-release version number (or -1 if no post-release segment is present). + """ + vc = str.split(ver, ".post") + return vc[0], int(vc[1] or 0) if len(vc) == 2 else None + + +def render_pep440_pre(pieces: Dict[str, Any]) -> str: + """TAG[.postN.devDISTANCE] -- No -dirty. + + Exceptions: + 1: no tags. 0.post0.devDISTANCE + """ + if pieces["closest-tag"]: if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] + # update the post release segment + tag_version, post_version = pep440_split_post(pieces["closest-tag"]) + rendered = tag_version + if post_version is not None: + rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"]) + else: + rendered += ".post0.dev%d" % (pieces["distance"]) + else: + # no commits, use the tag as the version + rendered = pieces["closest-tag"] else: # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] + rendered = "0.post0.dev%d" % pieces["distance"] return rendered -def render_pep440_post(pieces): +def render_pep440_post(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]+gHEX] . The ".dev0" means dirty. Note that .dev0 sorts backwards @@ -1301,12 +1659,41 @@ def render_pep440_post(pieces): return rendered -def render_pep440_old(pieces): +def render_pep440_post_branch(pieces: Dict[str, Any]) -> str: + """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] . + + The ".dev0" means not master branch. + + Exceptions: + 1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += ".post%d" % pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "g%s" % pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0.post%d" % pieces["distance"] + if pieces["branch"] != "master": + rendered += ".dev0" + rendered += "+g%s" % pieces["short"] + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def render_pep440_old(pieces: Dict[str, Any]) -> str: """TAG[.postDISTANCE[.dev0]] . The ".dev0" means dirty. - Eexceptions: + Exceptions: 1: no tags. 0.postDISTANCE[.dev0] """ if pieces["closest-tag"]: @@ -1323,7 +1710,7 @@ def render_pep440_old(pieces): return rendered -def render_git_describe(pieces): +def render_git_describe(pieces: Dict[str, Any]) -> str: """TAG[-DISTANCE-gHEX][-dirty]. Like 'git describe --tags --dirty --always'. @@ -1343,7 +1730,7 @@ def render_git_describe(pieces): return rendered -def render_git_describe_long(pieces): +def render_git_describe_long(pieces: Dict[str, Any]) -> str: """TAG-DISTANCE-gHEX[-dirty]. Like 'git describe --tags --dirty --always -long'. @@ -1363,7 +1750,7 @@ def render_git_describe_long(pieces): return rendered -def render(pieces, style): +def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]: """Render the given version pieces into the requested style.""" if pieces["error"]: return {"version": "unknown", @@ -1377,10 +1764,14 @@ def render(pieces, style): if style == "pep440": rendered = render_pep440(pieces) + elif style == "pep440-branch": + rendered = render_pep440_branch(pieces) elif style == "pep440-pre": rendered = render_pep440_pre(pieces) elif style == "pep440-post": rendered = render_pep440_post(pieces) + elif style == "pep440-post-branch": + rendered = render_pep440_post_branch(pieces) elif style == "pep440-old": rendered = render_pep440_old(pieces) elif style == "git-describe": @@ -1399,7 +1790,7 @@ class VersioneerBadRootError(Exception): """The project root directory is unknown or missing key files.""" -def get_versions(verbose=False): +def get_versions(verbose: bool = False) -> Dict[str, Any]: """Get the project version from whatever source is available. Returns dict with two keys: 'version' and 'full'. @@ -1414,7 +1805,7 @@ def get_versions(verbose=False): assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" handlers = HANDLERS.get(cfg.VCS) assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose + verbose = verbose or bool(cfg.verbose) # `bool()` used to avoid `None` assert cfg.versionfile_source is not None, \ "please set versioneer.versionfile_source" assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" @@ -1475,13 +1866,17 @@ def get_versions(verbose=False): "date": None} -def get_version(): +def get_version() -> str: """Get the short version string for this project.""" return get_versions()["version"] -def get_cmdclass(): - """Get the custom setuptools/distutils subclasses used by Versioneer.""" +def get_cmdclass(cmdclass: Optional[Dict[str, Any]] = None): + """Get the custom setuptools subclasses used by Versioneer. + + If the package uses a different cmdclass (e.g. one from numpy), it + should be provide as an argument. + """ if "versioneer" in sys.modules: del sys.modules["versioneer"] # this fixes the "python setup.py develop" case (also 'install' and @@ -1495,25 +1890,25 @@ def get_cmdclass(): # parent is protected against the child's "import versioneer". By # removing ourselves from sys.modules here, before the child build # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/warner/python-versioneer/issues/52 + # Also see https://github.com/python-versioneer/python-versioneer/issues/52 - cmds = {} + cmds = {} if cmdclass is None else cmdclass.copy() - # we add "version" to both distutils and setuptools - from distutils.core import Command + # we add "version" to setuptools + from setuptools import Command class cmd_version(Command): description = "report generated version string" - user_options = [] - boolean_options = [] + user_options: List[Tuple[str, str, str]] = [] + boolean_options: List[str] = [] - def initialize_options(self): + def initialize_options(self) -> None: pass - def finalize_options(self): + def finalize_options(self) -> None: pass - def run(self): + def run(self) -> None: vers = get_versions(verbose=True) print("Version: %s" % vers["version"]) print(" full-revisionid: %s" % vers.get("full-revisionid")) @@ -1523,7 +1918,7 @@ def run(self): print(" error: %s" % vers["error"]) cmds["version"] = cmd_version - # we override "build_py" in both distutils and setuptools + # we override "build_py" in setuptools # # most invocation pathways end up running build_py: # distutils/build -> build_py @@ -1538,18 +1933,25 @@ def run(self): # then does setup.py bdist_wheel, or sometimes setup.py install # setup.py egg_info -> ? + # pip install -e . and setuptool/editable_wheel will invoke build_py + # but the build_py command is not expected to copy any files. + # we override different "build_py" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.build_py import build_py as _build_py + if 'build_py' in cmds: + _build_py: Any = cmds['build_py'] else: - from distutils.command.build_py import build_py as _build_py + from setuptools.command.build_py import build_py as _build_py class cmd_build_py(_build_py): - def run(self): + def run(self) -> None: root = get_root() cfg = get_config_from_root(root) versions = get_versions() _build_py.run(self) + if getattr(self, "editable_mode", False): + # During editable installs `.py` and data files are + # not copied to build_lib + return # now locate _version.py in the new build/ directory and replace # it with an updated value if cfg.versionfile_build: @@ -1559,8 +1961,40 @@ def run(self): write_to_version_file(target_versionfile, versions) cmds["build_py"] = cmd_build_py + if 'build_ext' in cmds: + _build_ext: Any = cmds['build_ext'] + else: + from setuptools.command.build_ext import build_ext as _build_ext + + class cmd_build_ext(_build_ext): + def run(self) -> None: + root = get_root() + cfg = get_config_from_root(root) + versions = get_versions() + _build_ext.run(self) + if self.inplace: + # build_ext --inplace will only build extensions in + # build/lib<..> dir with no _version.py to write to. + # As in place builds will already have a _version.py + # in the module dir, we do not need to write one. + return + # now locate _version.py in the new build/ directory and replace + # it with an updated value + if not cfg.versionfile_build: + return + target_versionfile = os.path.join(self.build_lib, + cfg.versionfile_build) + if not os.path.exists(target_versionfile): + print(f"Warning: {target_versionfile} does not exist, skipping " + "version update. This can happen if you are running build_ext " + "without first running build_py.") + return + print("UPDATING %s" % target_versionfile) + write_to_version_file(target_versionfile, versions) + cmds["build_ext"] = cmd_build_ext + if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe + from cx_Freeze.dist import build_exe as _build_exe # type: ignore # nczeczulin reports that py2exe won't like the pep440-style string # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. # setup(console=[{ @@ -1569,7 +2003,7 @@ def run(self): # ... class cmd_build_exe(_build_exe): - def run(self): + def run(self) -> None: root = get_root() cfg = get_config_from_root(root) versions = get_versions() @@ -1593,12 +2027,12 @@ def run(self): if 'py2exe' in sys.modules: # py2exe enabled? try: - from py2exe.distutils_buildexe import py2exe as _py2exe # py3 + from py2exe.setuptools_buildexe import py2exe as _py2exe # type: ignore except ImportError: - from py2exe.build_exe import py2exe as _py2exe # py2 + from py2exe.distutils_buildexe import py2exe as _py2exe # type: ignore class cmd_py2exe(_py2exe): - def run(self): + def run(self) -> None: root = get_root() cfg = get_config_from_root(root) versions = get_versions() @@ -1619,14 +2053,51 @@ def run(self): }) cmds["py2exe"] = cmd_py2exe + # sdist farms its file list building out to egg_info + if 'egg_info' in cmds: + _egg_info: Any = cmds['egg_info'] + else: + from setuptools.command.egg_info import egg_info as _egg_info + + class cmd_egg_info(_egg_info): + def find_sources(self) -> None: + # egg_info.find_sources builds the manifest list and writes it + # in one shot + super().find_sources() + + # Modify the filelist and normalize it + root = get_root() + cfg = get_config_from_root(root) + self.filelist.append('versioneer.py') + if cfg.versionfile_source: + # There are rare cases where versionfile_source might not be + # included by default, so we must be explicit + self.filelist.append(cfg.versionfile_source) + self.filelist.sort() + self.filelist.remove_duplicates() + + # The write method is hidden in the manifest_maker instance that + # generated the filelist and was thrown away + # We will instead replicate their final normalization (to unicode, + # and POSIX-style paths) + from setuptools import unicode_utils + normalized = [unicode_utils.filesys_decode(f).replace(os.sep, '/') + for f in self.filelist.files] + + manifest_filename = os.path.join(self.egg_info, 'SOURCES.txt') + with open(manifest_filename, 'w') as fobj: + fobj.write('\n'.join(normalized)) + + cmds['egg_info'] = cmd_egg_info + # we override different "sdist" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.sdist import sdist as _sdist + if 'sdist' in cmds: + _sdist: Any = cmds['sdist'] else: - from distutils.command.sdist import sdist as _sdist + from setuptools.command.sdist import sdist as _sdist class cmd_sdist(_sdist): - def run(self): + def run(self) -> None: versions = get_versions() self._versioneer_generated_versions = versions # unless we update this, the command will keep using the old @@ -1634,7 +2105,7 @@ def run(self): self.distribution.metadata.version = versions["version"] return _sdist.run(self) - def make_release_tree(self, base_dir, files): + def make_release_tree(self, base_dir: str, files: List[str]) -> None: root = get_root() cfg = get_config_from_root(root) _sdist.make_release_tree(self, base_dir, files) @@ -1687,21 +2158,26 @@ def make_release_tree(self, base_dir, files): """ -INIT_PY_SNIPPET = """ +OLD_SNIPPET = """ from ._version import get_versions __version__ = get_versions()['version'] del get_versions """ +INIT_PY_SNIPPET = """ +from . import {0} +__version__ = {0}.get_versions()['version'] +""" -def do_setup(): - """Main VCS-independent setup function for installing Versioneer.""" + +def do_setup() -> int: + """Do main VCS-independent setup function for installing Versioneer.""" root = get_root() try: cfg = get_config_from_root(root) - except (EnvironmentError, configparser.NoSectionError, + except (OSError, configparser.NoSectionError, configparser.NoOptionError) as e: - if isinstance(e, (EnvironmentError, configparser.NoSectionError)): + if isinstance(e, (OSError, configparser.NoSectionError)): print("Adding sample versioneer config to setup.cfg", file=sys.stderr) with open(os.path.join(root, "setup.cfg"), "a") as f: @@ -1721,62 +2197,37 @@ def do_setup(): ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") + maybe_ipy: Optional[str] = ipy if os.path.exists(ipy): try: with open(ipy, "r") as f: old = f.read() - except EnvironmentError: + except OSError: old = "" - if INIT_PY_SNIPPET not in old: + module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0] + snippet = INIT_PY_SNIPPET.format(module) + if OLD_SNIPPET in old: + print(" replacing boilerplate in %s" % ipy) + with open(ipy, "w") as f: + f.write(old.replace(OLD_SNIPPET, snippet)) + elif snippet not in old: print(" appending to %s" % ipy) with open(ipy, "a") as f: - f.write(INIT_PY_SNIPPET) + f.write(snippet) else: print(" %s unmodified" % ipy) else: print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make sure both the top-level "versioneer.py" and versionfile_source - # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so - # they'll be copied into source distributions. Pip won't be able to - # install the package without this. - manifest_in = os.path.join(root, "MANIFEST.in") - simple_includes = set() - try: - with open(manifest_in, "r") as f: - for line in f: - if line.startswith("include "): - for include in line.split()[1:]: - simple_includes.add(include) - except EnvironmentError: - pass - # That doesn't cover everything MANIFEST.in can do - # (http://docs.python.org/2/distutils/sourcedist.html#commands), so - # it might give some false negatives. Appending redundant 'include' - # lines is safe, though. - if "versioneer.py" not in simple_includes: - print(" appending 'versioneer.py' to MANIFEST.in") - with open(manifest_in, "a") as f: - f.write("include versioneer.py\n") - else: - print(" 'versioneer.py' already in MANIFEST.in") - if cfg.versionfile_source not in simple_includes: - print(" appending versionfile_source ('%s') to MANIFEST.in" % - cfg.versionfile_source) - with open(manifest_in, "a") as f: - f.write("include %s\n" % cfg.versionfile_source) - else: - print(" versionfile_source already in MANIFEST.in") + maybe_ipy = None # Make VCS-specific changes. For git, this means creating/changing # .gitattributes to mark _version.py for export-subst keyword # substitution. - do_vcs_install(manifest_in, cfg.versionfile_source, ipy) + do_vcs_install(cfg.versionfile_source, maybe_ipy) return 0 -def scan_setup_py(): +def scan_setup_py() -> int: """Validate the contents of setup.py against Versioneer's expectations.""" found = set() setters = False @@ -1813,10 +2264,14 @@ def scan_setup_py(): return errors +def setup_command() -> NoReturn: + """Set up Versioneer and exit with appropriate error code.""" + errors = do_setup() + errors += scan_setup_py() + sys.exit(1 if errors else 0) + + if __name__ == "__main__": cmd = sys.argv[1] if cmd == "setup": - errors = do_setup() - errors += scan_setup_py() - if errors: - sys.exit(1) + setup_command()