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Update to use new openff rdkit parameterization #5

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11 changes: 7 additions & 4 deletions duck/utils/gen_system.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import numpy as np
import openforcefield.utils as utils
from openforcefield.typing.engines.smirnoff import forcefield_rdk
from openforcefield.typing.engines.smirnoff import ForceField
from openforcefield.topology import Molecule, Topology
from simtk import unit
import parmed, pkg_resources

Expand All @@ -20,8 +21,10 @@ def create_system_from_molecule_rdk(forcefield, mol, verbose=False):
positions : initial atomic positions (OpenMM)
"""
# Create system
topology = utils.generateTopologyFromRDKMol(mol)
system = forcefield.createSystem(topology, [mol], verbose=verbose)
molecule = Molecule.from_rdkit(mol, allow_undefined_stereo=True)
topology = Topology.from_molecules(molecule)
system = forcefield.create_openmm_system(topology, charge_from_molecules=[molecule])
topology = topology.to_openmm() # needed for call to parmed
# Get positions
coordinates = mol.GetConformer().GetPositions()
natoms = len(coordinates)
Expand All @@ -41,7 +44,7 @@ def generateSMIRNOFFStructureRDK(molecule):
"""
ff = pkg_resources.resource_filename('duck', "parameters/smirnoff99Frosst.offxml")
with open(ff) as ffxml:
mol_ff = forcefield_rdk.ForceField(ffxml)
mol_ff = ForceField(ffxml)
#TODO : integrate charges
# Can run this - should be already done
# os.system("antechamber -i " + mol2_file + " -fi mol2 -o " + out_file + " -fo mol2 -at sybyl -c bcc")
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