pmx Binding Free Energy Workflow

Owned by David Hahn
Last updated: Jan 26, 2022 by David Dotson
2 min read

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

 

Protocol 2022.01.26

mkdir working-session cd working-session python ../pmx/pmx/workflow/workflow1_parameterize_ligands.py -t cmet -f openff-1.0.0.offxml -p ../protein-ligand-benchmark/data/ -v -l lig_CHEMBL3402748_5300_8 python ../pmx/pmx/workflow/workflow2_make_perturbations.py -t cmet -f openff-1.0.0.offxml -p ../protein-ligand-benchmark/data/ -v -e edge_CHEMBL3402744_300_4_CHEMBL3402745_200_5 edge_CHEMBL3402747_3400_7_CHEMBL3402745_200_5 edge_CHEMBL3402747_3400_7_CHEMBL3402748_5300_8 edge_CHEMBL3402747_3400_7_CHEMBL3402751_2100_11 edge_CHEMBL3402748_5300_8_CHEMBL3402751_2100_11 edge_CHEMBL3402749_500_9_CHEMBL3402747_3400_7 edge_CHEMBL3402749_500_9_CHEMBL3402748_5300_8 edge_CHEMBL3402749_500_9_CHEMBL3402751_2100_11 edge_CHEMBL3402749_500_9_CHEMBL3402754_40_14 edge_CHEMBL3402750_400_10_CHEMBL3402747_3400_7 edge_CHEMBL3402750_400_10_CHEMBL3402748_5300_8 edge_CHEMBL3402750_400_10_CHEMBL3402749_500_9 edge_CHEMBL3402752_30000_12_CHEMBL3402744_300_4 edge_CHEMBL3402752_30000_12_CHEMBL3402747_3400_7 edge_CHEMBL3402752_30000_12_CHEMBL3402748_5300_8 edge_CHEMBL3402752_30000_12_CHEMBL3402749_500_9 edge_CHEMBL3402752_30000_12_CHEMBL3402754_40_14 edge_CHEMBL3402752_30000_12_CHEMBL3402755_4200_15 edge_CHEMBL3402753_200_13_CHEMBL3402748_5300_8 edge_CHEMBL3402753_200_13_CHEMBL3402754_40_14 edge_CHEMBL3402754_40_14_CHEMBL3402751_2100_11 edge_CHEMBL3402754_40_14_CHEMBL3402761_1_21 edge_CHEMBL3402755_4200_15_CHEMBL3402753_200_13 edge_CHEMBL3402755_4200_15_CHEMBL3402754_40_14 edge_CHEMBL3402755_4200_15_CHEMBL3402761_1_21 python ../pmx/pmx/workflow/workflow3_solvate.py -t cmet -f openff-1.0.0.offxml -p ../protein-ligand-benchmark/data/ -v -r 1 2 3 -e edge_CHEMBL3402744_300_4_CHEMBL3402745_200_5 edge_CHEMBL3402747_3400_7_CHEMBL3402745_200_5 edge_CHEMBL3402747_3400_7_CHEMBL3402748_5300_8 edge_CHEMBL3402747_3400_7_CHEMBL3402751_2100_11 edge_CHEMBL3402748_5300_8_CHEMBL3402751_2100_11 edge_CHEMBL3402749_500_9_CHEMBL3402747_3400_7 edge_CHEMBL3402749_500_9_CHEMBL3402748_5300_8 edge_CHEMBL3402749_500_9_CHEMBL3402751_2100_11 edge_CHEMBL3402749_500_9_CHEMBL3402754_40_14 edge_CHEMBL3402750_400_10_CHEMBL3402747_3400_7 edge_CHEMBL3402750_400_10_CHEMBL3402748_5300_8 edge_CHEMBL3402750_400_10_CHEMBL3402749_500_9 edge_CHEMBL3402752_30000_12_CHEMBL3402744_300_4 edge_CHEMBL3402752_30000_12_CHEMBL3402747_3400_7 edge_CHEMBL3402752_30000_12_CHEMBL3402748_5300_8 edge_CHEMBL3402752_30000_12_CHEMBL3402749_500_9 edge_CHEMBL3402752_30000_12_CHEMBL3402754_40_14 edge_CHEMBL3402752_30000_12_CHEMBL3402755_4200_15 edge_CHEMBL3402753_200_13_CHEMBL3402748_5300_8 edge_CHEMBL3402753_200_13_CHEMBL3402754_40_14 edge_CHEMBL3402754_40_14_CHEMBL3402751_2100_11 edge_CHEMBL3402754_40_14_CHEMBL3402761_1_21 edge_CHEMBL3402755_4200_15_CHEMBL3402753_200_13 edge_CHEMBL3402755_4200_15_CHEMBL3402754_40_14 edge_CHEMBL3402755_4200_15_CHEMBL3402761_1_21 # at this point, getting errors indicating TPR file isn't being generated