[Bug-gmx_MMPBSA]: gmx_mmpbsa not recognizing boron as atom type BG

Ridwan20-alt commented 1 year ago

Bug summary

gmx_mmpbsa not recognizing boron as atom type BG in my ligand

Terminal output

The following modules were not unloaded:
  (Use "module --force purge" to unload all):

  1) CCconfig         4) imkl/2020.1.217    7) libfabric/1.10.1
  2) gentoo/2020      5) intel/2020.1.217   8) openmpi/4.0.3
  3) gcccore/.9.3.0   6) ucx/1.8.0          9) StdEnv/2020

Due to MODULEPATH changes, the following have been reloaded:
  1) openmpi/4.0.3

Lmod is automatically replacing "intel/2020.1.217" with "gcc/9.3.0".

Lmod is automatically replacing "fftw-mpi/3.3.8" with "fftw/3.3.8".

-------------------------------------------------------------------------------
The following dependent module(s) are not currently loaded: fftw-mpi/3.3.8 (required by: gromacs/2022.3)
-------------------------------------------------------------------------------

Due to MODULEPATH changes, the following have been reloaded:
  1) openmpi/4.0.3

/var/spool/slurmd/job4481882/slurm_script: line 12: venv_gmxMMPBSA/bin/activate: No such file or directory
Starting run at: Thu 09 Mar 2023 08:45:07 PM EST
[INFO   ] Starting gmx_MMPBSA v1.6.0+5.g337926e3
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs step5_production.tpr -ci index2.ndx -cg 18 14 -ct md_0_300_fit.xtc -cp topol.top

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/cpptraj
[INFO   ] tleap found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/tleap
[INFO   ] parmchk2 found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/parmchk2
[INFO   ] sander found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/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 Protein_ZN2_UNK (18_14) 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 Protein_ZN2 (18) 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 UNK (14) 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 CHARMM force field topology format...
[INFO   ] Assigning PBRadii mbondi3 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 mbondi3 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 mbondi3 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 34 residues:
R:A:VAL:70  R:A:ILE:161 R:A:GLN:162 R:A:PHE:163 R:A:GLU:164 R:A:CYS:165 R:A:THR:193 R:A:PHE:194 R:A:GLY:195 R:A:PHE:196
R:A:GLU:197 R:A:PHE:213 R:A:ALA:214 R:A:THR:215 R:A:VAL:219 R:A:THR:220 R:A:HSD:223 R:A:GLU:224 R:A:HSD:227 R:A:VAL:258
R:A:GLU:262 R:A:GLU:351 R:A:ASN:362 R:A:ARG:363 R:A:THR:365 R:A:TYR:366 R:A:LEU:367 R:A:ASN:368 R:A:PHE:369 R:A:ASP:370
R:A:LYS:371 R:A:ALA:372 R::ZN2:418  L:B:UNK:419

[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   ] 200 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 1 CPUs...

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander
[INFO   ]   calculating complex contribution...

              0%|          | 0/200 [elapsed: 00:00 remaining: ?] bad atom type: BG
  File "/home/oladayo/venv_gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/oladayo/venv_gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/home/oladayo/venv_gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/oladayo/venv_gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/oladayo/venv_gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 284, in run
    raise CalcError(f'{self.program} failed with prmtop {self.prmtop}!')
CalcError: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander failed with prmtop COM.prmtop!
Exiting. All files have been retained.

gmx_MMPBSA.log

[INFO ] Starting gmx_MMPBSA v1.6.0+5.g337926e3 [DEBUG ] WDIR : /scratch/oladayo/Dynamics/LIG2/L12 [DEBUG ] AMBERHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21 [DEBUG ] PYTHON EXE : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.8.10/bin/python [DEBUG ] PYTHON VERSION: 3.9.6 (default, Jul 12 2021, 18:23:59) [GCC 9.3.0] [DEBUG ] MPI : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/gcc9/openmpi/4.0.3/bin/mpirun [DEBUG ] ParmEd : 3.4.3+11.g41cc9ab1 [DEBUG ] OS PLATFORM : Linux-3.10.0-1160.80.1.el7.x86_64-x86_64-with-glibc2.30 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #1 SMP Tue Nov 8 15:48:59 UTC 2022 [DEBUG ] OS PROCESSOR :

[INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs step5_production.tpr -ci index2.ndx -cg 18 14 -ct md_0_300_fit.xtc -cp topol.top

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/cpptraj [INFO ] tleap found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/tleap [INFO ] parmchk2 found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/parmchk2 [INFO ] sander found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/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... [DEBUG ] Running command: echo -e "name 18 GMXMMPBSA_REC\n name 14 GMXMMPBSA_LIG\n 18 | 14\n q\n" | /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx make_ndx -n index2.ndx -o _GMXMMPBSA_COM_index.ndx -f step5_production.tpr [DEBUG ] :-) GROMACS - gmx make_ndx, 2022.3-EasyBuild_4.6.0_ra6dbb4b22832c431590f725219d89d82c9946dba (-: [DEBUG ] [DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx [DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3 [DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L12 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n index2.ndx -o _GMXMMPBSA_COM_index.ndx -f step5_production.tpr [DEBUG ] [DEBUG ] [DEBUG ] Reading structure file [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] [DEBUG ] GROMACS reminds you: "If you open your mind too much, your brains will fall out." (Tim Minchin) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] [DEBUG ] 0 System : 70513 atoms [DEBUG ] 1 Protein : 6099 atoms [DEBUG ] 2 Protein-H : 3067 atoms [DEBUG ] 3 C-alpha : 377 atoms [DEBUG ] 4 Backbone : 1131 atoms [DEBUG ] 5 MainChain : 1507 atoms [DEBUG ] 6 MainChain+Cb : 1861 atoms [DEBUG ] 7 MainChain+H : 1869 atoms [DEBUG ] 8 SideChain : 4230 atoms [DEBUG ] 9 SideChain-H : 1560 atoms [DEBUG ] 10 Prot-Masses : 6099 atoms [DEBUG ] 11 non-Protein : 64414 atoms [DEBUG ] 12 Other : 64414 atoms [DEBUG ] 13 ZN2 : 1 atoms [DEBUG ] 14 UNK : 50 atoms [DEBUG ] 15 SOD : 60 atoms [DEBUG ] 16 CLA : 64 atoms [DEBUG ] 17 TIP3 : 64239 atoms [DEBUG ] 18 Protein_ZN2 : 6100 atoms [DEBUG ] [DEBUG ] nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups [DEBUG ] 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues [DEBUG ] 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help [DEBUG ] 'r': residue 'res' nr 'chain' char [DEBUG ] "name": group 'case': case sensitive 'q': save and quit [DEBUG ] 'ri': residue index [DEBUG ] [DEBUG ] > [DEBUG ] [DEBUG ] > [DEBUG ] [DEBUG ] > [DEBUG ] Copied index group 18 'GMXMMPBSA_REC' [DEBUG ] Copied index group 14 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 6100 50 -> 6150 [DEBUG ] [DEBUG ] 19 GMXMMPBSA_REC_GMXMMPBSA_LIG: 6150 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group Protein_ZN2_UNK (18_14) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx trjconv -f md_0_300_fit.xtc -s step5_production.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022.3-EasyBuild_4.6.0_ra6dbb4b22832c431590f725219d89d82c9946dba (-: [DEBUG ] [DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx [DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3 [DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L12 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f md_0_300_fit.xtc -s step5_production.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Group 0 ( System) has 70513 elements [DEBUG ] Group 1 ( Protein) has 6099 elements [DEBUG ] Group 2 ( Protein-H) has 3067 elements [DEBUG ] Group 3 ( C-alpha) has 377 elements [DEBUG ] Group 4 ( Backbone) has 1131 elements [DEBUG ] Group 5 ( MainChain) has 1507 elements [DEBUG ] Group 6 ( MainChain+Cb) has 1861 elements [DEBUG ] Group 7 ( MainChain+H) has 1869 elements [DEBUG ] Group 8 ( SideChain) has 4230 elements [DEBUG ] Group 9 ( SideChain-H) has 1560 elements [DEBUG ] Group 10 ( Prot-Masses) has 6099 elements [DEBUG ] Group 11 ( non-Protein) has 64414 elements [DEBUG ] Group 12 ( Other) has 64414 elements [DEBUG ] Group 13 ( ZN2) has 1 elements [DEBUG ] Group 14 ( GMXMMPBSA_LIG) has 50 elements [DEBUG ] Group 15 ( SOD) has 60 elements [DEBUG ] Group 16 ( CLA) has 64 elements [DEBUG ] Group 17 ( TIP3) has 64239 elements [DEBUG ] Group 18 ( GMXMMPBSA_REC) has 6100 elements [DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6150 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of md_0_300_fit.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 100.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Studying expands knowledge. Knowledge is power. Power corrupts. Corruption is a crime. Crime doesn't pay." (Anonymous) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 19: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [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 Protein_ZN2 (18) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo -e "18"| /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx trjconv -f md_0_300_fit.xtc -s step5_production.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022.3-EasyBuild_4.6.0_ra6dbb4b22832c431590f725219d89d82c9946dba (-: [DEBUG ] [DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx [DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3 [DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L12 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f md_0_300_fit.xtc -s step5_production.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Group 0 ( System) has 70513 elements [DEBUG ] Group 1 ( Protein) has 6099 elements [DEBUG ] Group 2 ( Protein-H) has 3067 elements [DEBUG ] Group 3 ( C-alpha) has 377 elements [DEBUG ] Group 4 ( Backbone) has 1131 elements [DEBUG ] Group 5 ( MainChain) has 1507 elements [DEBUG ] Group 6 ( MainChain+Cb) has 1861 elements [DEBUG ] Group 7 ( MainChain+H) has 1869 elements [DEBUG ] Group 8 ( SideChain) has 4230 elements [DEBUG ] Group 9 ( SideChain-H) has 1560 elements [DEBUG ] Group 10 ( Prot-Masses) has 6099 elements [DEBUG ] Group 11 ( non-Protein) has 64414 elements [DEBUG ] Group 12 ( Other) has 64414 elements [DEBUG ] Group 13 ( ZN2) has 1 elements [DEBUG ] Group 14 ( GMXMMPBSA_LIG) has 50 elements [DEBUG ] Group 15 ( SOD) has 60 elements [DEBUG ] Group 16 ( CLA) has 64 elements [DEBUG ] Group 17 ( TIP3) has 64239 elements [DEBUG ] Group 18 ( GMXMMPBSA_REC) has 6100 elements [DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6150 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of md_0_300_fit.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 100.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "I had a polynomial once. My doctor removed it." (Michael Grant) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 18: 'GMXMMPBSA_REC' [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 UNK (14) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo -e "14"| /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx trjconv -f md_0_300_fit.xtc -s step5_production.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022.3-EasyBuild_4.6.0_ra6dbb4b22832c431590f725219d89d82c9946dba (-: [DEBUG ] [DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx [DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3 [DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L12 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f md_0_300_fit.xtc -s step5_production.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Group 0 ( System) has 70513 elements [DEBUG ] Group 1 ( Protein) has 6099 elements [DEBUG ] Group 2 ( Protein-H) has 3067 elements [DEBUG ] Group 3 ( C-alpha) has 377 elements [DEBUG ] Group 4 ( Backbone) has 1131 elements [DEBUG ] Group 5 ( MainChain) has 1507 elements [DEBUG ] Group 6 ( MainChain+Cb) has 1861 elements [DEBUG ] Group 7 ( MainChain+H) has 1869 elements [DEBUG ] Group 8 ( SideChain) has 4230 elements [DEBUG ] Group 9 ( SideChain-H) has 1560 elements [DEBUG ] Group 10 ( Prot-Masses) has 6099 elements [DEBUG ] Group 11 ( non-Protein) has 64414 elements [DEBUG ] Group 12 ( Other) has 64414 elements [DEBUG ] Group 13 ( ZN2) has 1 elements [DEBUG ] Group 14 ( GMXMMPBSA_LIG) has 50 elements [DEBUG ] Group 15 ( SOD) has 60 elements [DEBUG ] Group 16 ( CLA) has 64 elements [DEBUG ] Group 17 ( TIP3) has 64239 elements [DEBUG ] Group 18 ( GMXMMPBSA_REC) has 6100 elements [DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6150 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of md_0_300_fit.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 100.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron Bradshaw) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 14: 'GMXMMPBSA_LIG' [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected CHARMM force field topology format... [INFO ] Assigning PBRadii mbondi3 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 mbondi3 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 mbondi3 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis... [INFO ] Selected 34 residues: R:A:VAL:70 R:A:ILE:161 R:A:GLN:162 R:A:PHE:163 R:A:GLU:164 R:A:CYS:165 R:A:THR:193 R:A:PHE:194 R:A:GLY:195 R:A:PHE:196 R:A:GLU:197 R:A:PHE:213 R:A:ALA:214 R:A:THR:215 R:A:VAL:219 R:A:THR:220 R:A:HSD:223 R:A:GLU:224 R:A:HSD:227 R:A:VAL:258 R:A:GLU:262 R:A:GLU:351 R:A:ASN:362 R:A:ARG:363 R:A:THR:365 R:A:TYR:366 R:A:LEU:367 R:A:ASN:368 R:A:PHE:369 R:A:ASP:370 R:A:LYS:371 R:A:ALA:372 R::ZN2:418 L:B:UNK:419

[INFO ] Cleaning normal complex trajectories... [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx trjconv -f md_0_300_fit.xtc -s step5_production.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2022.3-EasyBuild_4.6.0_ra6dbb4b22832c431590f725219d89d82c9946dba (-: [DEBUG ] [DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3/bin/gmx [DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2022.3 [DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L12 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f md_0_300_fit.xtc -s step5_production.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] Will write xtc: Compressed trajectory (portable xdr format): xtc [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Reading file step5_production.tpr, VERSION 2021.2 (single precision) [DEBUG ] Group 0 ( System) has 70513 elements [DEBUG ] Group 1 ( Protein) has 6099 elements [DEBUG ] Group 2 ( Protein-H) has 3067 elements [DEBUG ] Group 3 ( C-alpha) has 377 elements [DEBUG ] Group 4 ( Backbone) has 1131 elements [DEBUG ] Group 5 ( MainChain) has 1507 elements [DEBUG ] Group 6 ( MainChain+Cb) has 1861 elements [DEBUG ] Group 7 ( MainChain+H) has 1869 elements [DEBUG ] Group 8 ( SideChain) has 4230 elements [DEBUG ] Group 9 ( SideChain-H) has 1560 elements [DEBUG ] Group 10 ( Prot-Masses) has 6099 elements [DEBUG ] Group 11 ( non-Protein) has 64414 elements [DEBUG ] Group 12 ( Other) has 64414 elements [DEBUG ] Group 13 ( ZN2) has 1 elements [DEBUG ] Group 14 ( GMXMMPBSA_LIG) has 50 elements [DEBUG ] Group 15 ( SOD) has 60 elements [DEBUG ] Group 16 ( CLA) has 64 elements [DEBUG ] Group 17 ( TIP3) has 64239 elements [DEBUG ] Group 18 ( GMXMMPBSA_REC) has 6100 elements [DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6150 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of md_0_300_fit.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] Reading frame 1 time 100.000 -> frame 0 time 0.000

Reading frame 2 time 200.000 -> frame 1 time 100.000

Reading frame 3 time 300.000 -> frame 2 time 200.000

Reading frame 4 time 400.000 -> frame 3 time 300.000

Reading frame 5 time 500.000 -> frame 4 time 400.000

Reading frame 6 time 600.000 -> frame 5 time 500.000

Reading frame 7 time 700.000 -> frame 6 time 600.000

Reading frame 8 time 800.000 -> frame 7 time 700.000

Reading frame 9 time 900.000 -> frame 8 time 800.000

Reading frame 10 time 1000.000 -> frame 9 time 900.000

Reading frame 11 time 1100.000 -> frame 10 time 1000.000

Reading frame 12 time 1200.000 -> frame 11 time 1100.000

Reading frame 13 time 1300.000 -> frame 12 time 1200.000

Reading frame 14 time 1400.000 -> frame 13 time 1300.000

Reading frame 15 time 1500.000 -> frame 14 time 1400.000

Reading frame 16 time 1600.000 -> frame 15 time 1500.000

Reading frame 17 time 1700.000 -> frame 16 time 1600.000

Reading frame 18 time 1800.000 -> frame 17 time 1700.000

Reading frame 19 time 1900.000 -> frame 18 time 1800.000

Reading frame 20 time 2000.000 -> frame 19 time 1900.000

Reading frame 30 time 3000.000 -> frame 29 time 2900.000

Reading frame 40 time 4000.000 -> frame 39 time 3900.000

Reading frame 50 time 5000.000 -> frame 49 time 4900.000

Reading frame 60 time 6000.000 -> frame 59 time 5900.000

Reading frame 70 time 7000.000 -> frame 69 time 6900.000

Reading frame 80 time 8000.000 -> frame 79 time 7900.000

Reading frame 90 time 9000.000 -> frame 89 time 8900.000

Reading frame 100 time 10000.000 -> frame 99 time 9900.000

Reading frame 110 time 11000.000 -> frame 109 time 10900.000

Reading frame 120 time 12000.000 -> frame 119 time 11900.000

Reading frame 130 time 13000.000 -> frame 129 time 12900.000

Reading frame 140 time 14000.000 -> frame 139 time 13900.000

Reading frame 150 time 15000.000 -> frame 149 time 14900.000

Reading frame 160 time 16000.000 -> frame 159 time 15900.000

Reading frame 170 time 17000.000 -> frame 169 time 16900.000

Reading frame 180 time 18000.000 -> frame 179 time 17900.000

Reading frame 190 time 19000.000 -> frame 189 time 18900.000

Reading frame 200 time 20000.000 -> frame 199 time 19900.000

Reading frame 300 time 30000.000 -> frame 299 time 29900.000

Reading frame 400 time 40000.000 -> frame 399 time 39900.000

Reading frame 500 time 50000.000 -> frame 499 time 49900.000

Reading frame 600 time 60000.000 -> frame 599 time 59900.000

Reading frame 700 time 70000.000 -> frame 699 time 69900.000

Reading frame 800 time 80000.000 -> frame 799 time 79900.000

Reading frame 900 time 90000.000 -> frame 899 time 89900.000

Reading frame 1000 time 100000.000 -> frame 999 time 99900.000

Last frame 1000 time 100000.000
[DEBUG ] Last written: frame 1000 time 100000.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: ""What are the biological implications of your research?" - "Well, I simulate water." " (Petter Johansson) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 19: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] Building AMBER topologies from GROMACS files... Done.

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

[INFO ] 200 frames were processed by cpptraj for use in calculation. [INFO ] Starting calculations in 1 CPUs... [INFO ] Running calculations on normal system... [INFO ] Beginning GB calculations with /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander [INFO ] calculating complex contribution...

Operating system

No response

gmx_MMPBSA Version

No response

Python version

No response

Installation

None

Valdes-Tresanco-MS commented 1 year ago

This is a sander problem. Since computing sasa for decomposition requires the vdw radii (different from the solvation radii) of the atoms, then these are defined in sander's source code. Modifying it would be a bit difficult since you would have to add this information to the code and recompile it (does not work with AmberTools conda package) Please, check #326 if you want to carry out this modification. In this case, you can use PB (install the dev version since v1.6.0 have a bug related to PB decomposition)

Ridwan20-alt commented 1 year ago

Alright, thanks

Ridwan20-alt commented 1 year ago

Please do you know what I'm doing wrong I'm getting this error message while using gmx_mmpbsa_ana

ERROR:root:MMPBSA_Error Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is installed. Check the gmx_MMPBSA.log file to report the problem. Traceback (most recent call last): File "/scratch/oladayo/Dynamics/LIG2/L33/venv_gmxMMPBSA/bin/gmx_MMPBSA_ana", line 8, in sys.exit(gmxmmpbsa_ana()) File "/scratch/oladayo/Dynamics/LIG2/L33/venv_gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 126, in gmxmmpbsa_ana GMXMMPBSA_ERROR('Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is ' File "/scratch/oladayo/Dynamics/LIG2/L33/venv_gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in init raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.') GMXMMPBSA.exceptions.MMPBSA_Error: Could not import PyQt5/PyQt6. gmx_MMPBSA_ana will be disabled until PyQt5/PyQt6 is installed Check the gmx_MMPBSA.log file to report the problem.

Valdes-Tresanco-MS commented 1 year ago

To run gmx_MMPBSA_ana you must have PyQt5 or PyQt6 installed and support for opening desktop applications. In the case of HPCs, they do not have support for GUIs. In the WSL you must consult the Microsoft tutorials and have updated windows 10 or windows 11. You can install PyQt5 o PyQt6 as follow:

python -m pip install pyqt5

Ridwan20-alt commented 1 year ago

Okay, thank you

Valdes-Tresanco-MS commented 1 year ago

I closing this issue since the initial problem is solved. Feel free to open a new issue

Valdes-Tresanco-MS / gmx_MMPBSA