I've been trying to use ANI-2x to model the ligand during the simulation of a protein-ligand complex. I've been using the code below to set up the system.
prmtop = AmberPrmtopFile(prmtop_file)
inpcrd = AmberInpcrdFile(crd_file)
potential = MLPotential('ani2x')
ml_atoms = [atom.index for atom in prmtop.topology.atoms() if atom.residue.name == "MOL"]
mm_system = prmtop.createSystem(nonbondedMethod=PME,
nonbondedCutoff=1.0*unit.nanometers, constraints=HBonds, rigidWater=True,
ewaldErrorTolerance=0.0005)
ml_system = potential.createMixedSystem(prmtop.topology, mm_system, ml_atoms)
The last line in the code raises the following error:
Traceback (most recent call last):
File "/Users/victorprincipe/Local/project2021/local_tests/openmm_ani_test/md_ani.py", line 26, in <module>
ml_system = potential.createMixedSystem(prmtop.topology, mm_system, ml_atoms)
File "/Users/victorprincipe/miniconda3/envs/openmmani/lib/python3.9/site-packages/openmmml-1.0-py3.9.egg/openmmml/mlpotential.py", line 278, in createMixedSystem
self._impl.addForces(topology, newSystem, atomList, forceGroup, **args)
File "/Users/victorprincipe/miniconda3/envs/openmmani/lib/python3.9/site-packages/openmmml-1.0-py3.9.egg/openmmml/models/anipotential.py", line 85, in addForces
species = model.species_to_tensor(elements).unsqueeze(0)
File "/Users/victorprincipe/miniconda3/envs/openmmani/lib/python3.9/site-packages/torchani/models.py", line 165, in species_to_tensor
return self._species_to_tensor(*args, **kwargs) \
File "/Users/victorprincipe/miniconda3/envs/openmmani/lib/python3.9/site-packages/torchani/utils.py", line 237, in __call__
rev = [self.rev_species[s] for s in species]
File "/Users/victorprincipe/miniconda3/envs/openmmani/lib/python3.9/site-packages/torchani/utils.py", line 237, in <listcomp>
rev = [self.rev_species[s] for s in species]
KeyError: 'l'
I'm not sure why this is occurring, so any help would be greatly appreciated. I've also attached the prmtop and inpcrd files below. Thanks in advance!
Hi,
I've been trying to use ANI-2x to model the ligand during the simulation of a protein-ligand complex. I've been using the code below to set up the system.
The last line in the code raises the following error:
I'm not sure why this is occurring, so any help would be greatly appreciated. I've also attached the prmtop and inpcrd files below. Thanks in advance!
system_files.zip