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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
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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 |