Optimisation Demo Fails

[serbulent-av]

Hi,

Optmisation demo produces error during relaxation.

# python -m api.optimize

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2023-06-02 08:31:14::INFO::Openmm relaxing...
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Traceback (most recent call last):
  File "/opt/conda/envs/dyMEAN/envs/dyMEAN1/lib/python3.8/runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/opt/conda/envs/dyMEAN/envs/dyMEAN1/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/serbulent_antiverse_io/code/dyMEAN/api/optimize.py", line 223, in <module>
    optimize(
  File "/home/serbulent_antiverse_io/code/dyMEAN/api/optimize.py", line 194, in optimize
    openmm_relax(mod_pdb, mod_pdb,
  File "/home/serbulent_antiverse_io/code/dyMEAN/utils/relax.py", line 74, in openmm_relax
    modeller.addHydrogens(force_field)
  File "/opt/conda/envs/dyMEAN/envs/dyMEAN1/lib/python3.8/site-packages/openmm/app/modeller.py", line 998, in addHydrogens
    system = forcefield.createSystem(newTopology, rigidWater=False, nonbondedMethod=CutoffNonPeriodic)
  File "/opt/conda/envs/dyMEAN/envs/dyMEAN1/lib/python3.8/site-packages/openmm/app/forcefield.py", line 1218, in createSystem
    templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
  File "/opt/conda/envs/dyMEAN/envs/dyMEAN1/lib/python3.8/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 10 (LEU).  The set of atoms matches CLEU, but the bonds are different.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template

[kxz18]

Looks like it is because I extract the epitope into a PDB for openmm relaxing, which causes some errors on the template matching because of the discontinuous segments. I'm trying to figure out a solution.

[kxz18]

Hi, it should work now. I have to put the entire antigen into the compound for openmm relax, which will be slower but will not have the "no template found" problem again.

[serbulent-av]

Thank you very much it seems problem solved.