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Merge pull request #65 from openforcefield/opc_water
Add OPC water model
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@@ -7,3 +7,5 @@ dependencies: | |
| - openff-toolkit | ||
| - pytest | ||
| - pytest-cov | ||
| - pandas | ||
| - click | ||
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| @@ -1 +1,2 @@ | ||
| * `jc.csv`: Data taken from Table 5 in https://pubs.acs.org/doi/10.1021/jp8001614 | ||
| * `ionslm_126_opc.csv` taken from $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_opc in ambertools-22.0-py310h206695f |
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| element,opc_rmin2 (A),opc_eps (kcal/mol) | ||
| Li+,1.242,0.00216058 | ||
| Na+,1.467,0.02960343 | ||
| K+,1.702,0.13953816 | ||
| Rb+,1.818,0.2279546 | ||
| Cs+,1.96,0.35308749 | ||
| Tl+,1.66,0.11250137 | ||
| Cu+,1.18,0.00078213 | ||
| Ag+,1.316,0.00602547 | ||
| F-,1.84,0.24650465 | ||
| Cl-,2.36,0.6787887 | ||
| Br-,2.499,0.75971103 | ||
| I-,2.9,0.90300541 | ||
| Be2+,0.921,1.28e-06 | ||
| Cu2+,1.178,0.0007549 | ||
| Ni2+,1.197,0.00104974 | ||
| Pt2+,1.219,0.00150903 | ||
| Zn2+,1.219,0.00150903 | ||
| Co2+,1.263,0.00294683 | ||
| Pd2+,1.269,0.00321068 | ||
| Ag2+,1.305,0.00523385 | ||
| Cr2+,1.316,0.00602547 | ||
| Fe2+,1.323,0.00657749 | ||
| Mg2+,1.33,0.0071693 | ||
| V2+,1.334,0.00752608 | ||
| Mn2+,1.381,0.0128646 | ||
| Hg2+,1.381,0.0128646 | ||
| Cd2+,1.389,0.01400886 | ||
| Yb2+,1.602,0.08034231 | ||
| Ca2+,1.608,0.08337961 | ||
| Sn2+,1.625,0.09235154 | ||
| Pb2+,1.707,0.14295367 | ||
| Eu2+,1.753,0.17618319 | ||
| Sr2+,1.766,0.18612361 | ||
| Sm2+,1.766,0.18612361 | ||
| Ba2+,1.96,0.35308749 | ||
| Ra2+,1.96,0.35308749 | ||
| Al3+,1.25,0.00243637 | ||
| Fe3+,1.4,0.01570749 | ||
| Cr3+,1.336,0.00770969 | ||
| In3+,1.44,0.02322071 | ||
| Tl3+,1.483,0.03393126 | ||
| Y3+,1.575,0.06751391 | ||
| La3+,1.7,0.13818331 | ||
| Ce3+,1.725,0.15557763 | ||
| Pr3+,1.717,0.14990448 | ||
| Nd3+,1.662,0.11371963 | ||
| Sm3+,1.638,0.09957472 | ||
| Eu3+,1.646,0.10417397 | ||
| Gd3+,1.6,0.07934493 | ||
| Tb3+,1.608,0.08337961 | ||
| Dy3+,1.583,0.07117158 | ||
| Er3+,1.575,0.06751391 | ||
| Tm3+,1.575,0.06751391 | ||
| Lu3+,1.558,0.06014121 | ||
| Hf4+,1.461,0.02808726 | ||
| Zr4+,1.488,0.03537062 | ||
| Ce4+,1.683,0.12693448 | ||
| U4+,1.683,0.12693448 | ||
| Pu4+,1.658,0.11129023 | ||
| Th4+,1.704,0.14089951 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,44 @@ | ||
| import click | ||
| import pandas | ||
| from pathlib import Path | ||
|
|
||
| @click.command() | ||
| @click.argument( | ||
| "amber_frcmod_path", | ||
| type = click.Path(), | ||
| ) | ||
| def main(amber_frcmod_path): | ||
|
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| ion_nb_params = list() | ||
|
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||
| nonbonded = False | ||
|
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||
| with open(Path(amber_frcmod_path), "r") as amber_frcmod_file: | ||
| for line in amber_frcmod_file: | ||
|
|
||
| if line == '\n': | ||
| nonbonded = False | ||
|
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||
| if nonbonded: | ||
|
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| fields = line.split() | ||
|
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| ion_nb_params.append({ | ||
| "element": fields[0], | ||
| "opc_rmin2 (A)": float(fields[1]), | ||
| "opc_eps (kcal/mol)": float(fields[2]), | ||
| }) | ||
|
|
||
| if line.startswith('NONBON'): | ||
| nonbonded = True | ||
|
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| output_path = Path( | ||
| "openforcefields", "data", f"{Path(amber_frcmod_path).suffix[1:]}.csv" | ||
| ) | ||
| pandas.DataFrame(ion_nb_params).set_index("element").to_csv(output_path) | ||
|
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||
|
|
||
| if __name__ == "__main__": | ||
| main() | ||
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||
|
|
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| from openff.toolkit.typing.engines.smirnoff.forcefield import ForceField | ||
| from openff.toolkit.typing.engines.smirnoff.parameters import ( | ||
| ConstraintHandler, | ||
| ElectrostaticsHandler, | ||
| LibraryChargeHandler, | ||
| VirtualSiteHandler, | ||
| vdWHandler, | ||
| ) | ||
| from openff.units import unit | ||
| from openff.units.elements import SYMBOLS | ||
| from packaging import version | ||
| import pandas | ||
| from pathlib import Path | ||
|
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| # Data taken from ambertools-22.0-py310h206695f | ||
| # Water Lennard-Jones parameters and geometry from $AMBERHOME/dat/leap/parm/frcmod.opc | ||
| # Water hydrogen charge from $AMBERHOME/dat/leap/lib/solvents.lib | ||
| # Ion Lennard-Jones parameters from $AMBERHOME/dat/leap/parm/frcmod.ionslm_126_opc | ||
|
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| VERSION = version.Version("1.0.0") | ||
| OFFXML_PATH = Path("openforcefields", "offxml") | ||
|
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| ion_nb_params_df = pandas.read_csv("openforcefields/data/ionslm_126_opc.csv") | ||
|
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| opc = ForceField() | ||
|
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| opc_electrostatics = ElectrostaticsHandler(version=0.4, scale14=0.8333333333) | ||
| opc_library = LibraryChargeHandler(version=0.3) | ||
| opc_vdw = vdWHandler(version=0.3) | ||
| opc_constraints = ConstraintHandler(version=0.3) | ||
| opc_virtual_sites = VirtualSiteHandler(version=0.3) | ||
|
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| opc_vdw.add_parameter( | ||
| { | ||
| "smirks": "[#1]-[#8X2H2+0:1]-[#1]", | ||
| "epsilon": unit.Quantity(0.2128008130, unit.kilocalorie_per_mole), | ||
| "rmin_half": unit.Quantity(1.777167268, unit.angstrom), | ||
| "id": "n-opc-O", | ||
| } | ||
| ) | ||
| opc_vdw.add_parameter( | ||
| { | ||
| "smirks": "[#1:1]-[#8X2H2+0]-[#1]", | ||
| "epsilon": unit.Quantity(0.0, unit.kilocalorie_per_mole), | ||
| "rmin_half": unit.Quantity(1.0, unit.angstrom), | ||
| "id": "n-opc-H", | ||
| } | ||
| ) | ||
|
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||
| opc_library.add_parameter( | ||
| { | ||
| "smirks": "[#1]-[#8X2H2+0:1]-[#1]", | ||
| "charge1": unit.Quantity(0.0, unit.elementary_charge), | ||
| "id": "q-opc-O", | ||
| } | ||
| ) | ||
| opc_library.add_parameter( | ||
| { | ||
| "smirks": "[#1:1]-[#8X2H2+0]-[#1]", | ||
| "charge1": unit.Quantity(0.0, unit.elementary_charge), | ||
| "id": "q-opc-H", | ||
| } | ||
| ) | ||
|
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||
| opc_virtual_sites.add_parameter( | ||
| { | ||
| "type": "DivalentLonePair", | ||
| "smirks": "[#1:2]-[#8X2H2+0:1]-[#1:3]", | ||
| "match": "once", | ||
| "name": "EP", | ||
| "distance": unit.Quantity(-0.15939833, unit.angstrom), | ||
| "rmin_half": unit.Quantity(1.0, unit.angstrom), | ||
| "epsilon": unit.Quantity(0.0, unit.kilocalories_per_mole), | ||
| "outOfPlaneAngle": unit.Quantity(0.0, unit.degree), | ||
| "charge_increment1": unit.Quantity(0.0, unit.elementary_charge), | ||
| "charge_increment2": unit.Quantity(0.679142, unit.elementary_charge), | ||
| "charge_increment3": unit.Quantity(0.679142, unit.elementary_charge), | ||
| } | ||
| ) | ||
|
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||
| opc_constraints.add_parameter( | ||
| { | ||
| "smirks": "[#1:1]-[#8X2H2+0:2]-[#1]", | ||
| "id": "c-opc-H-O", | ||
| "distance": unit.Quantity(0.87243313 , unit.angstrom), | ||
| } | ||
| ) | ||
| opc_constraints.add_parameter( | ||
| { | ||
| "smirks": "[#1:1]-[#8X2H2+0]-[#1:2]", | ||
| "id": "c-opc-H-O-H", | ||
| "distance": unit.Quantity(1.37120510, unit.angstrom), | ||
| } | ||
| ) | ||
|
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||
| # Construct dict of element symbol to atomic number | ||
| _SYMBOLS_TO_ATOMIC_NUMBER = { | ||
| symbol: atomic_number for atomic_number, symbol in SYMBOLS.items() | ||
| } | ||
|
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| for _, row in ion_nb_params_df.iterrows(): | ||
|
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| ion_name = row["element"] | ||
|
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| # Handle variable length element names | ||
| if any(charge_str in ion_name for charge_str in ["2+", "3+", "4+"]): | ||
|
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| atomic_number = _SYMBOLS_TO_ATOMIC_NUMBER[ion_name[:-2]] | ||
| charge_sign = "+" | ||
| charge_magnitude = ion_name[-2] | ||
|
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| else: | ||
|
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| atomic_number = _SYMBOLS_TO_ATOMIC_NUMBER[ion_name[:-1]] | ||
| charge_sign = ion_name[-1] | ||
| charge_magnitude = "1" | ||
|
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| smirks = f"[#{atomic_number}X0{charge_sign}{charge_magnitude}:1]" | ||
|
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| opc_vdw.add_parameter( | ||
| { | ||
| "smirks": smirks, | ||
| "rmin_half": unit.Quantity(row["opc_rmin2 (A)"], unit.angstrom), | ||
| "epsilon": unit.Quantity( | ||
| row["opc_eps (kcal/mol)"], | ||
| unit.kilocalorie_per_mole, | ||
| ), | ||
| "id": f"n-ionslm-126-opc-{ion_name}" | ||
| } | ||
| ) | ||
|
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| opc_library.add_parameter( | ||
| { | ||
| "smirks": smirks, | ||
| "charge1": unit.Quantity( | ||
| int(f"{charge_sign}{charge_magnitude}"), unit.elementary_charge | ||
| ), | ||
| "id": f"q-ionslm-126-opc-{ion_name}" | ||
| } | ||
| ) | ||
|
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| for handler in [ | ||
| opc_vdw, | ||
| opc_library, | ||
| opc_electrostatics, | ||
| opc_constraints, | ||
| opc_virtual_sites, | ||
| ]: | ||
|
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| opc.register_parameter_handler(handler) | ||
|
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| opc.to_file(Path(OFFXML_PATH, "opc.offxml")) | ||
| opc.to_file(Path(OFFXML_PATH, f"opc-{VERSION}.offxml")) | ||
|
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