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Fix charge ordering in .prmtop files #1045

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Aug 29, 2024
Merged

Fix charge ordering in .prmtop files #1045

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f0e5d98
BUG: Fix charge ordering in `.prmtop` files
mattwthompson Aug 28, 2024
af9ba48
DOC: Update release history
mattwthompson Aug 29, 2024
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4 changes: 4 additions & 0 deletions docs/releasehistory.md
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Expand Up @@ -11,6 +11,10 @@ Dates are given in YYYY-MM-DD format.

Please note that all releases prior to a version 1.0.0 are considered pre-releases and many API changes will come before a stable release.

## 0.3.x

* #1045 Fixes a bug in which charges were sometimes misordered in `.prmtop` files.

## 0.3.30 - 2024-08

* #1039 Updates support of "cutoff" electrostatics in `.to_openmm` to better reflect what OpenMM supports. Set `"reaction-field"` to force the use of `CutoffPeriodic`, provided the vdW and electrostatic cutoff distances match. The potential/method `"cutoff"` is no longer supported but may be re-added in the future.
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20 changes: 20 additions & 0 deletions openff/interchange/_tests/test_issues.py
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Expand Up @@ -114,3 +114,23 @@ def test_issue_1031(monkeypatch):
# check a few atom names to ensure these didn't end up being empty sets
for atom_name in ("NE2", "H3", "HA", "CH3", "CA", "CB", "CE1"):
assert atom_name in openff_atom_names


def test_issue_1033(water, sage):
"""Test issue/PR 1033, in which charges were not ordered topologically."""
pytest.importorskip("parmed")

interchange = sage.create_interchange(
Topology.from_molecules(3 * [water]),
)

interchange.to_prmtop("test.prmtop")

structure = parmed.load_file("test.prmtop")

# atoms should be ordered OHH OHH OHH, charges should be as well
assert 3 * [
(8, -0.834),
(1, 0.417),
(1, 0.417),
] == [(atom.atomic_number, atom.charge) for atom in structure.atoms]
12 changes: 9 additions & 3 deletions openff/interchange/interop/amber/export/_export.py
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Expand Up @@ -22,7 +22,7 @@
UnsupportedExportError,
UnsupportedMixingRuleError,
)
from openff.interchange.models import PotentialKey
from openff.interchange.models import PotentialKey, TopologyKey


def _write_text_blob(file, blob):
Expand Down Expand Up @@ -514,9 +514,15 @@ def to_prmtop(interchange: "Interchange", file_path: Path | str):
_write_text_blob(prmtop, text_blob)

prmtop.write("%FLAG CHARGE\n" "%FORMAT(5E16.8)\n")
electro = interchange["Electrostatics"]
charges = [
charge.m_as(unit.e) * AMBER_COULOMBS_CONSTANT
for charge in interchange["Electrostatics"].charges.values()
charge * AMBER_COULOMBS_CONSTANT
for charge in [
electro.charges[TopologyKey(atom_indices=(index,))].m_as(
unit.elementary_charge,
)
for index in range(interchange.topology.n_atoms)
]
]
text_blob = "".join([f"{val:16.8E}" for val in charges])
_write_text_blob(prmtop, text_blob)
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