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Experiments with expanded ensembles to explore chemical space

Home Page: http://perses.readthedocs.io

License: MIT License

Shell 0.04% Python 85.77% TeX 6.09% Jupyter Notebook 8.10%

perses's People

Contributors

ajsilveira avatar dominicrufa avatar glass-w avatar hannahbrucemacdonald avatar ijpulidos avatar jaimergp avatar jchodera avatar lnaden avatar mcwitt avatar mikemhenry avatar pgrinaway avatar sauravmaheshkar avatar schallerdavid avatar steven-albanese avatar zhang-ivy avatar

perses's Issues

Cannot pass protein and ligand Molecule object

Motivation:
Parameterize protein-ligand self-consistently with espaloma.

Details:
Try to handle the protein as a single residue openff.topology.Molecule object and append it with the other small molecules. Then load the list of Molecules into openmmforcefields.generators.SystemGenerator but get the following error.

Problem:

Traceback (most recent call last):
  File "openmm/app/internal/compiled.pyx", line 223, in openmm.app.internal.compiled._findAtomMatches
  File "openmm/app/internal/compiled.pyx", line 223, in openmm.app.internal.compiled._findAtomMatches
  File "openmm/app/internal/compiled.pyx", line 223, in openmm.app.internal.compiled._findAtomMatches
  [Previous line repeated 995 more times]
  File "openmm/app/internal/compiled.pyx", line 212, in openmm.app.internal.compiled._findAtomMatches
  File "openmm/app/internal/compiled.pyx", line 200, in openmm.app.internal.compiled._getAtomMatchCandidates
RecursionError: maximum recursion depth exceeded in comparison

Reproduce
Perses branch: sandbox
input.tar.gz.zip: input files
stderr_stdout.tar.gz.zip: log and error message
myenv.yml.zip: conda environment

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