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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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Bug-gmx_MMPBSA]: Alanine scanning #317

Closed Ding-qh closed 1 year ago

Ding-qh commented 1 year ago

My Question is...

[INFO ] Starting gmx_MMPBSA v1.5.6 [INFO ] Command-line mpirun -np 10 gmx_MMPBSA MPI -O -i mmpbsa.in -cs /data/MD/1e883af9-6ac2-4890-82c3-94d3ee51012d/md.tpr -ci index_custom_group.ndx -cg 19 18 -ct md_pdc.xtc -cp /data/MD/1e883af9-6ac2-4890-82c3-94d3ee51012d/system.top -eo FINAL_RESULTS_MMPBSA.csv -nogui

[INFO ] Checking mmpbsa.in input file... [INFO ] Checking mmpbsa.in input file...Done.

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /data/PRG/tools/molecular_simulation/apps/amber20/bin/cpptraj [INFO ] tleap found! Using /data/PRG/tools/molecular_simulation/apps/amber20/bin/tleap [INFO ] parmchk2 found! Using /data/PRG/tools/molecular_simulation/apps/amber20/bin/parmchk2 [INFO ] sander found! Using /data/PRG/tools/molecular_simulation/apps/amber20/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /usr/local/gromacs/bin/gmx [INFO ] Checking external programs...Done.

[INFO ] Building AMBER topologies from GROMACS files... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [INFO ] Normal Complex: Saving group 19_18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [INFO ] No receptor structure file was defined. Using ST approach... [INFO ] Using receptor structure from complex to generate AMBER topology [INFO ] Normal Receptor: Saving group 19 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [INFO ] No ligand structure file was defined. Using ST approach... [INFO ] Using ligand structure from complex to generate AMBER topology [INFO ] Normal Ligand: Saving group 18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected Amber/OPLS force field topology format... [WARNING] 6 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1 [INFO ] Assigning PBRadii mbondi2 to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Building Mutant Complex Topology... [INFO ] Mutating B/6 ARG by ALA [INFO ] Setting intdiel = intdiel_positive = 5 for Alanine scanning [INFO ] Setting intdiel = indi = intdiel_positive = 5 for Alanine scanning [INFO ] Assigning PBRadii mbondi2 to Mutant Complex... [INFO ] Writing Mutant Complex AMBER topology... [INFO ] Detecting mutation in Receptor. Building Mutant Receptor topology... [INFO ] Assigning PBRadii mbondi2 to Mutant Receptor... [INFO ] Writing Mutant Receptor AMBER topology... [INFO ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis... [INFO ] Selected 50 residues: L:A:PHE:22 L:A:SER:25 L:A:SER:26 L:A:LEU:27 L:A:SER:29 L:A:TRP:30 L:A:TYR:32 L:A:ASN:33 L:A:TRP:51 L:A:LEU:55 L:A:ASN:85 L:A:TYR:109 L:A:ASP:188 L:A:VAL:325 L:A:HID:327 L:A:PRO:328 L:A:THR:329 L:A:ALA:330 L:A:TRP:331 L:A:ASP:332 L:A:LEU:333 L:A:GLY:334 L:A:PHE:338 L:A:HIP:356 L:A:GLU:357 L:A:HID:360 L:A:TYR:363 L:A:ASH:364 L:A:TYR:367 L:A:PHE:372 L:A:LEU:373 L:A:ARG:375 L:A:ASN:376 L:A:GLY:377 L:A:ASN:379 L:A:GLU:380 L:A:HIE:383 L:A:GLU:384 L:A:PHE:486 L:A:HIE:487 L:A:ASN:490 L:A:TYR:492 L:A:ARG:496 L:A:TYR:497 R:B:LYS:1 R:B:GLU:2 R:B:PRO:3 R:B:TYR:4 R:B:ARG:5 R:B:ARG:6

[INFO ] Cleaning normal complex trajectories... [INFO ] Building AMBER topologies from GROMACS files... Done.

[INFO ] Loading and checking parameter files for compatibility... [INFO ] Preparing trajectories for simulation...

[INFO ] Mutating trajectories... File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa app.file_setup() File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 154, in filesetup , mutant_residue = make_mutant_trajectories(INPUT, FILES, self.mpi_rank, self.external_progs['cpptraj'], File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 334, in make_mutant_trajectories com_mut.MutateTraj(pre + 'mutant_complex.%s.%d' % (trj_suffix, rank)) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/alamdcrd.py", line 276, in MutateTraj temp_holder.append(words[i]) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa app.file_setup() File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 154, in filesetup , mutant_residue = make_mutant_trajectories(INPUT, FILES, self.mpi_rank, self.external_progs['cpptraj'], File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 334, in make_mutant_trajectories com_mut.MutateTraj(pre + 'mutant_complex.%s.%d' % (trj_suffix, rank)) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/alamdcrd.py", line 276, in MutateTraj temp_holder.append(words[i]) IndexError: list index out of range Error occurred on rank 3. File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa app.file_setup() File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 154, in filesetup , mutant_residue = make_mutant_trajectories(INPUT, FILES, self.mpi_rank, self.external_progs['cpptraj'], File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 334, in make_mutant_trajectories com_mut.MutateTraj(pre + 'mutant_complex.%s.%d' % (trj_suffix, rank)) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/alamdcrd.py", line 276, in MutateTraj temp_holder.append(words[i]) IndexError: list index out of range Error occurred on rank 4. File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa app.file_setup() File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 154, in filesetup , mutant_residue = make_mutant_trajectories(INPUT, FILES, self.mpi_rank, self.external_progs['cpptraj'], File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 334, in make_mutant_trajectories com_mut.MutateTraj(pre + 'mutant_complex.%s.%d' % (trj_suffix, rank)) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/alamdcrd.py", line 276, in MutateTraj temp_holder.append(words[i]) IndexError: list index out of range Error occurred on rank 5. Exiting. All files have been retained. File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa app.file_setup() File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 154, in filesetup , mutant_residue = make_mutant_trajectories(INPUT, FILES, self.mpi_rank, self.external_progs['cpptraj'], File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 334, in make_mutant_trajectories com_mut.MutateTraj(pre + 'mutant_complex.%s.%d' % (trj_suffix, rank)) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/alamdcrd.py", line 276, in MutateTraj temp_holder.append(words[i]) IndexError: list index out of range Error occurred on rank 8. Exiting. All files have been retained. IndexError: list index out of range Error occurred on rank 2. Exiting. All files have been retained. Exiting. All files have been retained. application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3 Exiting. All files have been retained. application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5 File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 103, in gmxmmpbsa app.file_setup() File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 154, in filesetup , mutant_residue = make_mutant_trajectories(INPUT, FILES, self.mpi_rank, self.external_progs['cpptraj'], File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_trajs.py", line 334, in make_mutant_trajectories com_mut.MutateTraj(pre + 'mutant_complex.%s.%d' % (trj_suffix, rank)) File "/data/PRG/tools/molecular_simulation/apps/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/alamdcrd.py", line 276, in MutateTraj temp_holder.append(words[i]) IndexError: list index out of range Error occurred on rank 6. Exiting. All files have been retained. application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6

I was trying to make an alanine scanning on the end of six-peptide (B:6), but reported the error as described above. mmpbsa.in file connect is as follow: image

Valdes-Tresanco-MS commented 1 year ago

Please, use the latest version (v1.5.7). We fixed this bug through 4b4813e8c5dc72fd11d90d6b53581f4a1cd80761 and 96dc892585937b1a5348e4a12de4c2eb00c33aba

python -m pip install gmx_MMPBSA -U
Ding-qh commented 1 year ago

Please, use the latest version (v1.5.7). We fixed this bug through 4b4813e and 96dc892

python -m pip install gmx_MMPBSA -U

thanks for you help! The problem has already been settled.