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Step 1. command: curl https://gpcrdb.org/structure/homology_models/pth2r_human_active_full/download_pdb -o ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.zip executable: bash input files: output files: ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.zip Step 2. command: unzip ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.zip executable: bash input files: ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.zip <-- from Step 1. output files: ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.pdb Step 3. command: sed -i -e '1,217d;3502,4387d' ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.pdb executable: bash input files: ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.pdb <-- from Step 2. output files: ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.pdb Step 4. command: curl https://opm-assets.storage.googleapis.com/pdb/7f16.pdb -o PTH2R_opm.pdb executable: bash input files: output files: PTH2R_opm.pdb Step 5. command: sed -i -e '2,761d;3835,13708d' PTH2R_opm.pdb executable: bash input files: PTH2R_opm.pdb <-- from Step 4. output files: PTH2R_opm.pdb Step 6. command: echo -e '0 | 0 \n q' | gmx confrms -f1 PTH2R_opm.pdb -f2 ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.pdb -name -one -o PTH2R_fit.pdb executable: bash input files: ClassB1_pth2r_human_Active_AF_2022-08-16_GPCRdb.pdb <-- from Step 3. PTH2R_opm.pdb <-- from Step 5. output files: PTH2R_fit.pdb Step 7. command: -f PTH2R_fit.pdb -o PTH2R_opm.top -x PTH2R_opm.cg.pdb -ff martini3001 -nt -dssp mkdssp -elastic -p backbone -maxwarn 1 -mutate HSD:HIS -mutate HSP:HIH -ignh -cys auto -scfix executable: martinize2 input files: PTH2R_fit.pdb <-- from Step 6. output files: PTH2R_opm.top PTH2R_opm.cg.pdb molecule_0.itp Step 8. command: insane_custom.py -f PTH2R_opm.cg.pdb -o solvated.gro -p system.top -pbc rectangular -box 18,18,17 -u POPC:25 -u DOPC:25 -u POPE:8 -u DOPE:7 -u CHOL:25 -u DPG3:10 -l POPC:5 -l DOPC:5 -l POPE:20 -l DOPE:20 -l CHOL:25 -l POPS:8 -l DOPS:7 -l POP2:10 -sol W executable: python input files: insane_custom.py PTH2R_opm.cg.pdb <-- from Step 7. output files: solvated.gro system.top Step 9. command: sed -i -e "1 s/^/#include \"toppar\/martini_v3.0.0.itp\"\n#include \"toppar\/martini_v3.0.0_ions_v1.itp\"\n#include \"toppar\/martini_v3.0.0_solvents_v1.itp\"\n#include \"toppar\/martini_v3.0.0_phospholipids_v1.itp\"\n#include \"martini_v3.0_sterols_v1.0.itp\"\n#include \"POP2.itp\"\n#include \"molecule_0.itp\"\n#include \"gm3_final.itp\"\n/" -e "s/Protein/molecule_0/" -e "s/#include \"martini.itp\"/\n/" system.top executable: bash input files: system.top <-- from Step 8. output files: system.top Step 10. command: sed -i -e "s/1000 1000 1000/POSRES_FC POSRES_FC POSRES_FC/g" -e "s/#ifdef POSRES/#ifdef POSRES\n#ifndef POSRES_FC\n#define POSRES_FC 1000.00\n#endif/" molecule_0.itp executable: bash input files: molecule_0.itp <-- from Step 7. output files: molecule_0.itp Step 11. command: gmx grompp -f ions.mdp -c solvated.gro -p system.top -o ions.tpr executable: gmx input files: ions.mdp solvated.gro <-- from Step 8. system.top <-- from Step 9. gm3_final.itp molecule_0.itp martini_v3.0_sterols_v1.0.itp POP2.itp output files: grompp.out ions.tpr Step 12. command: gmx genion -s ions.tpr -o solvated_ions.gro -p system.top -pname NA -nname CL -conc 0.15 -neutral true -instructions inputs_genion.txt executable: gmx input files: inputs_genion.txt ions.tpr <-- from Step 11. system.top <-- from Step 9. output files: genion.out solvated_ions.gro system.top Step 13. command: gmx make_ndx -f solvated_ions.gro -o index.ndx -instructions inputs_index.txt executable: gmx input files: inputs_index.txt solvated_ions.gro <-- from Step 12. output files: make_ndx.out index.ndx Step 14. command: gmx grompp -f step6.0_minimization.mdp -c solvated_ions.gro -r solvated_ions.gro -p system.top -o step6.0_minimization.tpr -n index.ndx -maxwarn 1 executable: gmx input files: step6.0_minimization.mdp solvated_ions.gro <-- from Step 12. system.top <-- from Step 12. POP2.itp martini_v3.0_sterols_v1.0.itp gm3_final.itp molecule_0.itp solvated_ions.gro index.ndx output files: grompp.out step6.0_minimization.tpr Step 15. command: gmx mdrun -s step6.0_minimization.tpr -c step6.0_minimization.gro -e step6.0_minimization.edr -g step6.0_minimization.log -o step6.0_minimization.trr -xvg none executable: gmx input files: step6.0_minimization.tpr <-- from Step 14. output files: mdrun.out step6.0_minimization.gro step6.0_minimization.edr step6.0_minimization.log step6.0_minimization.trr Step 16. command: gmx grompp -f step6.1_minimization.mdp -o step6.1_minimization.tpr -c step6.0_minimization.gro -r solvated_ions.gro -p system.top -n index.ndx -maxwarn 1 executable: gmx input files: step6.1_minimization.mdp step6.0_minimization.gro <-- from Step 15. system.top <-- from Step 12. gm3_final.itp molecule_0.itp POP2.itp martini_v3.0_sterols_v1.0.itp solvated_ions.gro index.ndx output files: grompp.out step6.1_minimization.tpr Step 17. command: gmx mdrun -s step6.1_minimization.tpr -c step6.1_minimization.gro -e step6.0_minimization.edr -g step6.1_minimization.log -o step6.1_minimization.trr -xvg none executable: gmx input files: step6.1_minimization.tpr <-- from Step 16. output files: mdrun.out step6.1_minimization.gro step6.0_minimization.edr step6.1_minimization.log step6.1_minimization.trr Step 18. command: gmx grompp -f step6.2_equilibration.mdp -o step6.2_equilibration.tpr -c step6.1_minimization.gro -r solvated_ions.gro -p system.top -n index.ndx -maxwarn 1 executable: gmx input files: step6.2_equilibration.mdp step6.1_minimization.gro <-- from Step 17. system.top <-- from Step 12. gm3_final.itp martini_v3.0_sterols_v1.0.itp POP2.itp molecule_0.itp solvated_ions.gro index.ndx output files: grompp.out step6.2_equilibration.tpr Step 19. command: gmx mdrun -s step6.2_equilibration.tpr -c step6.2_equilibration.gro -e step6.1_minimization.edr -g step6.2_equilibration.log -o step6.2_equilibration.trr -x step6.2_equilibration.xtc -xvg none executable: gmx input files: step6.2_equilibration.tpr <-- from Step 18. output files: mdrun.out step6.2_equilibration.gro step6.1_minimization.edr step6.2_equilibration.log step6.2_equilibration.xtc Step 20. command: gmx grompp -f step6.3_equilibration.mdp -o step6.3_equilibration.tpr -c step6.2_equilibration.gro -r solvated_ions.gro -p system.top -n index.ndx -maxwarn 1 executable: gmx input files: step6.3_equilibration.mdp step6.2_equilibration.gro <-- from Step 19. system.top <-- from Step 12. gm3_final.itp POP2.itp martini_v3.0_sterols_v1.0.itp molecule_0.itp solvated_ions.gro index.ndx output files: grompp.out step6.3_equilibration.tpr Step 21. command: executable: input files: 01_Min.in parm7 rst7 output files: sander.out 01_Min.out 01_Min.mdinfo 01_Min.ncrst Step 22. command: executable: input files: 01_Min.in parm7 rst7 output files: sander.out 01_Min.out 01_Min.mdinfo 01_Min.ncrst Step 23. command: executable: input files: 01_Min.in parm7 rst7 output files: sander.out 01_Min.out 01_Min.mdinfo 01_Min.ncrst Step 24. command: executable: input files: 01_Min.in parm7 rst7 output files: sander.out 01_Min.out 01_Min.mdinfo 01_Min.ncrst
Pull Request Test Coverage Report for Build 9197786654Details
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Pull Request Test Coverage Report for Build 9197786654Details
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jkalayan
deleted the
131-simple-text-output-of-the-command-run-what-input-files-were-used-to-perform-the-command-and-what-output-files-were-produced-by-the-command-that-can-be-viewed-in-the-interpreter
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