openff-forcefields
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openforcefield
sulfate angle parameters are incorrectly identified
Describe the bug When attempting to parameterize a sulfate smiles of "[O-]S(=O)(=O)[O-]", the resulting topology does not assign all angles to 109.5 degrees.
To Reproduce
import openmm
from openff.toolkit import ForceField, Molecule, unit
from openff.interchange import Interchange
from openff.interchange.components._packmol import RHOMBIC_DODECAHEDRON, pack_box
ligand = Molecule.from_smiles("[O-]S(=O)(=O)[O-]")
topology = pack_box(
molecules=[ligand],
number_of_copies=[1],
box_vectors=3.5 * RHOMBIC_DODECAHEDRON * unit.nanometer,
)
topology.n_molecules, topology.box_vectors, topology.get_positions().shape
sage = ForceField("openff-2.2.1.offxml")
interchange: Interchange = Interchange.from_smirnoff(force_field=sage, topology=topology)
interchange.topology.n_atoms, interchange.box, interchange.positions.shape
integrator = openmm.LangevinIntegrator(
300 * openmm.unit.kelvin,
1 / openmm.unit.picosecond,
1 * openmm.unit.femtoseconds,
)
simulation = interchange.to_openmm_simulation(integrator=integrator)
print("\n### angles")
bonded = [f for f in simulation.system.getForces() if isinstance(f, openmm.openmm.HarmonicAngleForce)][0]
for i in range(bonded.getNumAngles()):
print(bonded.getAngleParameters(i))
Output
### angles
[0, 1, 2, Quantity(value=1.8712080163342617, unit=radian), Quantity(value=1000.8227065747888, unit=kilojoule/(mole*radian**2))]
[0, 1, 3, Quantity(value=1.8712080163342617, unit=radian), Quantity(value=1000.8227065747888, unit=kilojoule/(mole*radian**2))]
[0, 1, 4, Quantity(value=1.8712080163342617, unit=radian), Quantity(value=1000.8227065747888, unit=kilojoule/(mole*radian**2))]
[2, 1, 3, Quantity(value=2.1025946571403775, unit=radian), Quantity(value=789.2336085207944, unit=kilojoule/(mole*radian**2))]
[2, 1, 4, Quantity(value=1.8712080163342617, unit=radian), Quantity(value=1000.8227065747888, unit=kilojoule/(mole*radian**2))]
[3, 1, 4, Quantity(value=1.8712080163342617, unit=radian), Quantity(value=1000.8227065747888, unit=kilojoule/(mole*radian**2))]
Computing environment (please complete the following information): mac M1
$ conda list
# packages in environment at ...:
#
# Name Version Build Channel
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tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tinydb 4.8.2 pyhd8ed1ab_1 conda-forge
tk 8.6.13 h1abcd95_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_1 conda-forge
tornado 6.4.2 py312h01d7ebd_0 conda-forge
tqdm 4.67.1 pyhd8ed1ab_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_1 conda-forge
types-python-dateutil 2.9.0.20241206 pyhd8ed1ab_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_1 conda-forge
typing_extensions 4.12.2 pyha770c72_1 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge
tzdata 2025a h78e105d_0 conda-forge
unicodedata2 16.0.0 py312h01d7ebd_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_1 conda-forge
urllib3 2.3.0 pyhd8ed1ab_0 conda-forge
validators 0.34.0 pyhd8ed1ab_1 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_1 conda-forge
webcolors 24.11.1 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_3 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
wget 1.25.0 h3a17b82_0
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
widgetsnbextension 4.0.13 pyhd8ed1ab_1 conda-forge
xmltodict 0.14.2 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 h6e16a3a_0 conda-forge
xorg-libsm 1.2.6 h6e16a3a_0 conda-forge
xorg-libx11 1.8.12 h217831a_0 conda-forge
xorg-libxau 1.0.12 h6e16a3a_0 conda-forge
xorg-libxdmcp 1.1.5 h00291cd_0 conda-forge
xorg-libxext 1.3.6 h00291cd_0 conda-forge
xorg-libxt 1.3.1 h6e16a3a_0 conda-forge
xz 5.6.4 h46256e1_1
yaml 0.2.5 h0d85af4_2 conda-forge
zeromq 4.3.5 h7130eaa_7 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zlib 1.2.13 h87427d6_6 conda-forge
zlib-ng 2.0.7 h6c40b1e_0
zstandard 0.23.0 py312h01d7ebd_1 conda-forge
zstd 1.5.6 h138b38a_0
Additional context Add any other context about the problem here.
Thanks for the report, Chris! I can reproduce and see the issue of incorrectly perceiving O=S=O:
import openmm
from openff.toolkit import ForceField, Molecule, unit
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
IPythonConsole.ipython_useSVG=True
ligand = Molecule.from_smiles("[O-]S(=O)(=O)[O-]")
ff = ForceField("openff-2.2.1.offxml")
angles = ff.label_molecules(ligand.to_topology())[0]["Angles"]
for indices, parameter in angles.items():
elements = [ligand.atoms[i].symbol for i in indices]
label = "-".join(f"{el}{i + 1}" for el, i in zip(elements, indices))
print(f"{label} | {parameter.id} -- {parameter.angle}, {parameter.k}")
O1-S2-O3 | a32 -- 107.212321927 degree, 239.2023677282 kilocalorie_per_mole / radian ** 2
O1-S2-O4 | a32 -- 107.212321927 degree, 239.2023677282 kilocalorie_per_mole / radian ** 2
O1-S2-O5 | a32 -- 107.212321927 degree, 239.2023677282 kilocalorie_per_mole / radian ** 2
O3-S2-O4 | a31 -- 120.4697998809 degree, 188.6313595891 kilocalorie_per_mole / radian ** 2
O3-S2-O5 | a32 -- 107.212321927 degree, 239.2023677282 kilocalorie_per_mole / radian ** 2
O4-S2-O5 | a32 -- 107.212321927 degree, 239.2023677282 kilocalorie_per_mole / radian ** 2
This should be something we can fix with a more specific angle SMIRKS.
I think you will also need more specific bond parameters too, unless those already exist. Because all 4 bonds in the sulfate ion should also be identical.
@bannanc In 2.2.1 at least they are identical -- all 4 get picked up by b59, with the relatively general SMIRKS "[#16X4,#16X3:1]~[#8X1:2]".