No template find for residue...

[GustavoG9]

Hi, I have been trying to parametrize a small molecule using OpenMM. I have tried looking in the FQA section, but I still haven't been able to find a solution to my problem. Every time I try to run, I fall into the following error:

Did not recognize residue MOL; did you forget to call .add_molecules() to add it? Traceback (most recent call last): File "/oscar/home/ggramire/Polyelectrolyte/nonpolarizableff/polye_gaff2_amber/OPC/dimer_IE/openff-2.1.0/test.py", line 19, in <module> system = forcefield.createSystem(pdbfile.topology) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/users/ggramire/anaconda/openmm/lib/python3.11/site-packages/openmm/app/forcefield.py", line 1218, in createSystem templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/users/ggramire/anaconda/openmm/lib/python3.11/site-packages/openmm/app/forcefield.py", line 1433, in _matchAllResiduesToTemplates raise ValueError('No template found for residue %d (%s). %s For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template' % (res.index+1, res.name, _findMatchErrors(self, res))) ValueError: No template found for residue 1 (MOL). This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template

I attached the pdb file at the end. This is the script used, any help would be highly appreciated. Thank you in advance.

``

Create an OpenFF Molecule object for benzene from SMILES

from openff.toolkit.topology import Molecule
molecule = Molecule.from_smiles('CC(=O)OCCN+(C)CC1=CC=CC=C1')
###Create the SMIRNOFF template generator with the default installed force field (openff-1.0.0)
from openmmforcefields.generators import SMIRNOFFTemplateGenerator
smirnoff = SMIRNOFFTemplateGenerator(molecules=molecule)
smirnoff.add_molecules(molecule)

Create an OpenMM ForceField object with AMBER ff14SB and TIP3P with compatible ions

from openmm.app import ForceField

forcefield = ForceField('amber14/protein.ff14SB.xml')
forcefield = ForceField('amoeba2018.xml')

Register the SMIRNOFF template generator

forcefield.registerTemplateGenerator(smirnoff.generator)

from openmm.app import PDBFile
pdbfile = PDBFile('monomer.pdb')
system = forcefield.createSystem(pdbfile.topology)

print("Parametrization successful")
``
monomer.txt

[peastman]

You first load the Amber14 force field, but then throw it out and overwrite it with AMOEBA 2018:

forcefield = ForceField('amber14/protein.ff14SB.xml')
forcefield = ForceField('amoeba2018.xml')

The OpenFF force field isn't compatible with AMOEBA.