Installation
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protein-ligand-benchmark
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conda create -n pmxworkflow -c conda-forge -c omnia python=3.7 openforcefield numpy pandas future git-lfs pint |
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conda activate pmxworkflow |
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git lfs clone |
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https://github.com/openforcefield/ |
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protein-ligand-benchmark.git cd protein-ligand-benchmark conda env update --file environment.yml pip install -e . cd .. |
pmx workflow (part of dfhahn’s pmx fork)
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git clone https://github.com/dfhahn/pmx/ |
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cd pmx |
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git checkout --track origin/py3 |
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pip install -e . |
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cd .. |
Protocol
python ~/src/pmx/pmx/workflow/workflow1_parameterize_ligands.py -t cmet -f openff-1.0.0.offxml -p ./ -v -l lig_CHEMBL3402748_5300_8
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