Installation

protein-ligand-benchmark

conda create -n pmxworkflow -c conda-forge -c omnia python=3.7 openforcefield numpy pandas future git-lfs pint
conda activate pmxworkflow
git lfs clone https://github.com/openforcefield/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)

git clone https://github.com/dfhahn/pmx/
cd pmx
git checkout --track origin/py3
pip install -e .
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

python ~/src/pmx/pmx/workflow/workflow2_make_perturbations.py -t pde10 -f openff-1.0.0.offxml -p ./ -v -e edge_5687_4147 edge_3032_4096 edge_8041_4147 edge_5687_1056 edge_0340_4754 edge_7395_1939 edge_5687_8161 edge_5544_4147 edge_8041_0738 edge_5973_4096 edge_4147_0395 edge_3484_2750 edge_1939_7846 edge_2750_6221 edge_5973_4754 edge_3484_4189 edge_1038_5687 edge_4415_3032 edge_3806_4147 edge_1423_4754 edge_4147_5973 edge_1801_4147 edge_2750_5973 edge_8041_1939 edge_0340_0738 edge_3032_8041

python ~/src/pmx/pmx/workflow/workflow3_solvate.py -t pde10 -f openff-1.0.0.offxml -p ./ -v -r 1 2 3 <-e edge_5687_4147 edge_3032_4096 ...>

python ~/pmx/pmx/workflow/workflow4_write_scripts.py -t pde10 -f openff-1.0.0.offxml -p ./ -v -r 1 2 3 -s em nvt eq morphes -e edge_5687_4147

python ~/pmx/pmx/workflow/workflow5_submit_simulations.py -t pde10 -f openff-1.0.0.offxml -p ./ -v -r 1 2 3 -q sge <-e edge_5687_4147 edge_3032_4096 >

python ~/pmx/pmx/workflow/workflow6_check_simulations.py -t ros1 -f openff-1.0.0.offxml -p ./ -v -r 2 3 -s em eq nvt morphes -q sge

python ~/src/pmx/pmx/workflow/workflow7_analyse.py -t pde10 -f openff-1.0.0.offxml -p ./ -v -r 1 2 3