Error when trying to create mixed system

[victorprincipe]

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.

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!

system_files.zip