Closed Ridwan20-alt closed 1 year ago
marioernestovaldes
commented
1 year ago I see you're using version 1.5.0.3... That version is outdated. Please update to the latest version (v1.6.0) and see if the error persists...
pip install gmx-MMPBSA -U
Ridwan20-alt
commented
1 year ago Thank you for your prompt answer. I have used the latest version, and the error message still persists as pasted below:
[INFO ] Starting gmx_MMPBSA v1.6.0 [DEBUG ] WDIR : /scratch/oladayo/Dynamics/LIG2/L32/L32 [DEBUG ] AMBERHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21 [DEBUG ] PYTHON EXE : /scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.8.10 (default, Jun 16 2021, 14:20:20) [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+5.g16fb2364 [DEBUG ] OS PLATFORM : Linux-3.10.0-1160.80.1.el7.x86_64-x86_64-with-glibc2.2.5 [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 str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 18 -ct com_traj.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |Sample input file for PB calculation [DEBUG ] |This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use the input files as recommended [DEBUG ] |in the Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the [DEBUG ] |parameters according to what is better for your system. [DEBUG ] | [DEBUG ] |&general [DEBUG ] |sys_name="Prot-Lig-CHARMM", [DEBUG ] |startframe=5, [DEBUG ] |endframe=9, [DEBUG ] |# In gmx_MMPBSA v1.5.0 we have added a new PB radii set named charmm_radii. This radii set should be used only [DEBUG ] |# with systems prepared with CHARMM force fields. Uncomment the line below to use charmm_radii set [DEBUG ] |#PBRadii=7, [DEBUG ] |/ [DEBUG ] |&pb [DEBUG ] |# radiopt=0 is recommended which means using radii from the prmtop file for both the PB calculation and for the NP [DEBUG ] |# calculation [DEBUG ] |istrng=0.15, fillratio=4.0, radiopt=0 [DEBUG ] |/-------------------------------------------------------------- [DEBUG ] [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/2021.4/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 1 GMXMMPBSA_REC\n name 18 GMXMMPBSA_LIG\n 1 | 18\n q\n" | /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx make_ndx -n index_mod_gromacs.ndx -o _GMXMMPBSA_COM_index.ndx -f str_noLP.pdb
[DEBUG ] :-) GROMACS - gmx make_ndx, 2021.4 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx make_ndx, version 2021.4
[DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx
[DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4
[DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L32/L32
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index_mod_gromacs.ndx -o _GMXMMPBSA_COM_index.ndx -f str_noLP.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ]
[DEBUG ] GROMACS reminds you: "The best model of a cat is another cat..., specially the same cat." (Arturo Rosenblueth)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 70506 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 : 64407 atoms
[DEBUG ] 12 Other : 64407 atoms
[DEBUG ] 13 ZN2 : 1 atoms
[DEBUG ] 14 UNK : 46 atoms
[DEBUG ] 15 SOD : 60 atoms
[DEBUG ] 16 CLA : 64 atoms
[DEBUG ] 17 TIP3 : 64236 atoms
[DEBUG ] 18 lig : 44 atoms
[DEBUG ] 19 Protein_lig : 6143 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 1 'GMXMMPBSA_REC'
[DEBUG ] Copied index group 18 'GMXMMPBSA_LIG'
[DEBUG ] Merged two groups with OR: 6099 44 -> 6143
[DEBUG ]
[DEBUG ] 20 GMXMMPBSA_REC_GMXMMPBSA_LIG: 6143 atoms
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group Protein_lig (1_18) 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/2021.4/bin/gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG ] :-) GROMACS - gmx editconf, 2021.4 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx editconf, version 2021.4
[DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx
[DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4
[DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L32/L32
[DEBUG ] Command line:
[DEBUG ] gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Select a group for output:
[DEBUG ] Group 0 ( System) has 70506 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) 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 64407 elements
[DEBUG ] Group 12 ( Other) has 64407 elements
[DEBUG ] Group 13 ( ZN2) has 1 elements
[DEBUG ] Group 14 ( UNK) has 46 elements
[DEBUG ] Group 15 ( SOD) has 60 elements
[DEBUG ] Group 16 ( CLA) has 64 elements
[DEBUG ] Group 17 ( TIP3) has 64236 elements
[DEBUG ] Group 18 ( GMXMMPBSA_LIG) has 44 elements
[DEBUG ] Group 19 ( Protein_lig) has 6143 elements
[DEBUG ] Group 20 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6143 elements
[DEBUG ] Select a group:
[ERROR ] MMPBSA_Error /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf failed when querying com_traj.xtc.
Check the gmx_MMPBSA.log file to report the problem.
marioernestovaldes
commented
1 year ago It's odd because the xtc is not processed with editconf... did you run the tests from gmx_MMPBSA?
Ridwan20-alt
commented
1 year ago I don't understand what you meant by that sorry. Yes, I ran the tests , and it was successful:
[INFO ] Starting gmx_MMPBSA v1.6.0 [DEBUG ] WDIR : /scratch/oladayo/Dynamics/LIG2/L32/L32/gmx_MMPBSA_test/examples/Protein_ligand_LPH_atoms_CHARMMff [DEBUG ] AMBERHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21 [DEBUG ] PYTHON EXE : /scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.8.10 (default, Jun 16 2021, 14:20:20) [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+5.g16fb2364 [DEBUG ] OS PLATFORM : Linux-3.10.0-1160.80.1.el7.x86_64-x86_64-with-glibc2.2.5 [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 str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 17 -ct com_traj.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |Sample input file for GB calculation [DEBUG ] |#This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use the input files as recommended in the [DEBUG ] |#Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the parameters [DEBUG ] |#according to what is better for your system. [DEBUG ] | [DEBUG ] |&general [DEBUG ] |sys_name="Prot-Lig-ST", [DEBUG ] |startframe=5, [DEBUG ] |endframe=9, [DEBUG ] |solvated_trajectory=0, [DEBUG ] |# In gmx_MMPBSA v1.5.0 we have added a new PB radii set named charmm_radii. This radii set should be used only [DEBUG ] |# with systems prepared with CHARMM force fields. Uncomment the line below to use charmm_radii set [DEBUG ] |#PBRadii=7, [DEBUG ] |/ [DEBUG ] |&pb [DEBUG ] |# radiopt=0 is recommended which means using radii from the prmtop file [DEBUG ] |# for both the PB calculation and for the NP calculation [DEBUG ] | [DEBUG ] |istrng=0.15, fillratio=1.250, radiopt=0, inp=1, [DEBUG ] |/ [DEBUG ] |-------------------------------------------------------------- [DEBUG ] [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/2021.4/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 1 GMXMMPBSA_REC\n name 17 GMXMMPBSA_LIG\n 1 | 17\n q\n" | /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx make_ndx -n index_mod_gromacs.ndx -o _GMXMMPBSA_COM_index.ndx -f str_noLP.pdb
[DEBUG ] :-) GROMACS - gmx make_ndx, 2021.4 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx make_ndx, version 2021.4
[DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx
[DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4
[DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L32/L32/gmx_MMPBSA_test/examples/Protein_ligand_LPH_atoms_CHARMMff
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index_mod_gromacs.ndx -o _GMXMMPBSA_COM_index.ndx -f str_noLP.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ]
[DEBUG ] GROMACS reminds you: "If your experiment needs a statistician, you need a better experiment." (Ernest Rutherford)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 70483 atoms
[DEBUG ] 1 Protein : 5580 atoms
[DEBUG ] 2 Protein-H : 2817 atoms
[DEBUG ] 3 C-alpha : 334 atoms
[DEBUG ] 4 Backbone : 1002 atoms
[DEBUG ] 5 MainChain : 1335 atoms
[DEBUG ] 6 MainChain+Cb : 1654 atoms
[DEBUG ] 7 MainChain+H : 1654 atoms
[DEBUG ] 8 SideChain : 3926 atoms
[DEBUG ] 9 SideChain-H : 1482 atoms
[DEBUG ] 10 Prot-Masses : 5580 atoms
[DEBUG ] 11 non-Protein : 64903 atoms
[DEBUG ] 12 Other : 64903 atoms
[DEBUG ] 13 3G5 : 32 atoms
[DEBUG ] 14 CLA : 62 atoms
[DEBUG ] 15 SOD : 63 atoms
[DEBUG ] 16 TIP3 : 64746 atoms
[DEBUG ] 17 lig : 30 atoms
[DEBUG ] 18 Protein_lig : 5610 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 1 'GMXMMPBSA_REC'
[DEBUG ] Copied index group 17 'GMXMMPBSA_LIG'
[DEBUG ] Merged two groups with OR: 5580 30 -> 5610
[DEBUG ]
[DEBUG ] 19 GMXMMPBSA_REC_GMXMMPBSA_LIG: 5610 atoms
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group Protein_lig (1_17) 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/2021.4/bin/gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG ] :-) GROMACS - gmx editconf, 2021.4 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx editconf, version 2021.4
[DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx
[DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4
[DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L32/L32/gmx_MMPBSA_test/examples/Protein_ligand_LPH_atoms_CHARMMff
[DEBUG ] Command line:
[DEBUG ] gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Select a group for output:
[DEBUG ] Group 0 ( System) has 70483 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 5580 elements
[DEBUG ] Group 2 ( Protein-H) has 2817 elements
[DEBUG ] Group 3 ( C-alpha) has 334 elements
[DEBUG ] Group 4 ( Backbone) has 1002 elements
[DEBUG ] Group 5 ( MainChain) has 1335 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1654 elements
[DEBUG ] Group 7 ( MainChain+H) has 1654 elements
[DEBUG ] Group 8 ( SideChain) has 3926 elements
[DEBUG ] Group 9 ( SideChain-H) has 1482 elements
[DEBUG ] Group 10 ( Prot-Masses) has 5580 elements
[DEBUG ] Group 11 ( non-Protein) has 64903 elements
[DEBUG ] Group 12 ( Other) has 64903 elements
[DEBUG ] Group 13 ( 3G5) has 32 elements
[DEBUG ] Group 14 ( CLA) has 62 elements
[DEBUG ] Group 15 ( SOD) has 63 elements
[DEBUG ] Group 16 ( TIP3) has 64746 elements
[DEBUG ] Group 17 ( GMXMMPBSA_LIG) has 30 elements
[DEBUG ] Group 18 ( Protein_lig) has 5610 elements
[DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 5610 elements
[DEBUG ] Select a group:
[DEBUG ] GROMACS reminds you: "Is it the invisible chemistry stuff?" (Frida Hyvonen)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility.
[DEBUG ] Read 5610 atoms
[DEBUG ] Volume: 694.847 nm^3, corresponds to roughly 312600 electrons
[DEBUG ] No velocities found
[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 (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG ] Running command: echo -e "1"| /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_REC.pdb
[DEBUG ] :-) GROMACS - gmx editconf, 2021.4 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx editconf, version 2021.4
[DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx
[DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4
[DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L32/L32/gmx_MMPBSA_test/examples/Protein_ligand_LPH_atoms_CHARMMff
[DEBUG ] Command line:
[DEBUG ] gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_REC.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Select a group for output:
[DEBUG ] Group 0 ( System) has 70483 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 5580 elements
[DEBUG ] Group 2 ( Protein-H) has 2817 elements
[DEBUG ] Group 3 ( C-alpha) has 334 elements
[DEBUG ] Group 4 ( Backbone) has 1002 elements
[DEBUG ] Group 5 ( MainChain) has 1335 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1654 elements
[DEBUG ] Group 7 ( MainChain+H) has 1654 elements
[DEBUG ] Group 8 ( SideChain) has 3926 elements
[DEBUG ] Group 9 ( SideChain-H) has 1482 elements
[DEBUG ] Group 10 ( Prot-Masses) has 5580 elements
[DEBUG ] Group 11 ( non-Protein) has 64903 elements
[DEBUG ] Group 12 ( Other) has 64903 elements
[DEBUG ] Group 13 ( 3G5) has 32 elements
[DEBUG ] Group 14 ( CLA) has 62 elements
[DEBUG ] Group 15 ( SOD) has 63 elements
[DEBUG ] Group 16 ( TIP3) has 64746 elements
[DEBUG ] Group 17 ( GMXMMPBSA_LIG) has 30 elements
[DEBUG ] Group 18 ( Protein_lig) has 5610 elements
[DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 5610 elements
[DEBUG ] Select a group:
[DEBUG ] GROMACS reminds you: "Is it the invisible chemistry stuff?" (Frida Hyvonen)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility.
[DEBUG ] Read 5610 atoms
[DEBUG ] Volume: 694.847 nm^3, corresponds to roughly 312600 electrons
[DEBUG ] No velocities found
[DEBUG ] Selected 1: '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 lig (17) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG ] Running command: echo -e "17"| /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_LIG.pdb
[DEBUG ] :-) GROMACS - gmx editconf, 2021.4 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx editconf, version 2021.4
[DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx
[DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4
[DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L32/L32/gmx_MMPBSA_test/examples/Protein_ligand_LPH_atoms_CHARMMff
[DEBUG ] Command line:
[DEBUG ] gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_LIG.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Select a group for output:
[DEBUG ] Group 0 ( System) has 70483 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 5580 elements
[DEBUG ] Group 2 ( Protein-H) has 2817 elements
[DEBUG ] Group 3 ( C-alpha) has 334 elements
[DEBUG ] Group 4 ( Backbone) has 1002 elements
[DEBUG ] Group 5 ( MainChain) has 1335 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1654 elements
[DEBUG ] Group 7 ( MainChain+H) has 1654 elements
[DEBUG ] Group 8 ( SideChain) has 3926 elements
[DEBUG ] Group 9 ( SideChain-H) has 1482 elements
[DEBUG ] Group 10 ( Prot-Masses) has 5580 elements
[DEBUG ] Group 11 ( non-Protein) has 64903 elements
[DEBUG ] Group 12 ( Other) has 64903 elements
[DEBUG ] Group 13 ( 3G5) has 32 elements
[DEBUG ] Group 14 ( CLA) has 62 elements
[DEBUG ] Group 15 ( SOD) has 63 elements
[DEBUG ] Group 16 ( TIP3) has 64746 elements
[DEBUG ] Group 17 ( GMXMMPBSA_LIG) has 30 elements
[DEBUG ] Group 18 ( Protein_lig) has 5610 elements
[DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 5610 elements
[DEBUG ] Select a group:
[DEBUG ] GROMACS reminds you: "Is it the invisible chemistry stuff?" (Frida Hyvonen)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility.
[DEBUG ] Read 5610 atoms
[DEBUG ] Volume: 694.847 nm^3, corresponds to roughly 312600 electrons
[DEBUG ] No velocities found
[DEBUG ] Selected 17: '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 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 AMBER topologies from GROMACS files... Done.
[INFO ] Loading and checking parameter files for compatibility... [INFO ] Preparing trajectories for simulation...
[INFO ] 5 frames were processed by cpptraj for use in calculation. [INFO ] Starting calculations in 1 CPUs... [INFO ] Running calculations on normal system... [INFO ] Beginning PB calculations with /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander [INFO ] calculating complex contribution... [INFO ] calculating receptor contribution... [INFO ] calculating ligand contribution... [INFO ] Parsing results to output files...
[INFO ] Timing: [INFO ] Total GROMACS setup time: 0.194 min. [INFO ] Total AMBER setup time: 0.018 min. [INFO ] Creating trajectories with cpptraj: 0.009 min. [INFO ] Total calculation time: 4.976 min. [INFO ] Total PB calculation time: 4.679 min. [INFO ] Statistics calculation & output writing: 0.002 min. [INFO ] Total time taken: 5.200 min.
[INFO ] Finalizing gmx_MMPBSA: [ERROR ] = 0; [WARNING] = 0 Check the gmx_MMPBSA.log file for more details...
[INFO ] Thank you for using gmx_MMPBSA. Please consider supporting gmx_MMPBSA by citing our publication: Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. J Chem Theory Comput., 2021, 17 (10):6281-6291. Epub 2021 Sep 29. PMID: 34586825. https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645
Also consider citing MMPBSA.py: Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. J. Chem. Theory Comput., 2012, 8 (9) pp 3314-3321
[INFO ] Opening gmx_MMPBSA_ana to analyze results...
[ERROR ] Unable to start gmx_MMPBSA_ana... [INFO ] Finalized...
marioernestovaldes
commented
1 year ago well, I suspect it should be the new files you are using... could you please send me the files to take a look and see if I can identify the issue?
Ridwan20-alt
commented
1 year ago Please which of the files should I send ?
marioernestovaldes
commented
1 year ago pdb, index file, topology files and just few frames of the trajectory
Ridwan20-alt
commented
1 year ago Here we go ....
From: Mario E. Valdés-Tresanco @.> Sent: Thursday, March 2, 2023 3:56 PM To: Valdes-Tresanco-MS/gmx_MMPBSA @.> Cc: Ridwan Sulaimon @.>; Author @.> Subject: Re: [Valdes-Tresanco-MS/gmx_MMPBSA] [Bug-gmx_MMPBSA]: gmx editconf failed when querying com_traj.xtc (Issue #350)
pdb, index file, topology files and just few frames of the trajectory
— Reply to this email directly, view it on GitHubhttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FValdes-Tresanco-MS%2Fgmx_MMPBSA%2Fissues%2F350%23issuecomment-1452601399&data=05%7C01%7Cridwan.sulaimon%40mail.concordia.ca%7Cbf43bf25da8d40e01f9408db1b68f357%7C5569f185d22f4e139850ce5b1abcd2e8%7C0%7C0%7C638133909804900915%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FEbRqba4tII3Ii%2BXB30ykF79bjZj%2FqnS%2BQkceWgggAA%3D&reserved=0, or unsubscribehttps://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FA6HP2ECMV7C4ID56Y7YNB3LW2EJQDANCNFSM6AAAAAAVNW3474&data=05%7C01%7Cridwan.sulaimon%40mail.concordia.ca%7Cbf43bf25da8d40e01f9408db1b68f357%7C5569f185d22f4e139850ce5b1abcd2e8%7C0%7C0%7C638133909804900915%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bunhK2elyEtdx9ZmCV8YeMIdyF4W8qDsiZT5GBRC2hw%3D&reserved=0. You are receiving this because you authored the thread.Message ID: @.***>
Ridwan20-alt
commented
1 year ago Sent to your email
Ridwan20-alt
commented
1 year ago One last file please toppar.zip
marioernestovaldes
commented
1 year ago havne't received any files yet...
Ridwan20-alt
commented
1 year ago Really... toppar1.zip Let me send it again
Ridwan20-alt
commented
1 year ago Have you received it now ?
marioernestovaldes
commented
1 year ago Yes, working on it
marioernestovaldes
commented
1 year ago The index file is somehow corrupted and it gives segmentation fault error when you try to extract any group beyond the 14th.
for example, see this output
Command line:
gmx editconf -f str_noLP.pdb -n index_mod_gromacs.ndx -o lig.pdb
Note that major changes are planned in future for editconf, to improve usability and utility.
Read 6143 atoms
Volume: 753.571 nm^3, corresponds to roughly 339100 electrons
No velocities found
Select a group for output:
Group 0 ( System) has 70506 elements
Group 1 ( Protein) has 6099 elements
Group 2 ( Protein-H) has 3067 elements
Group 3 ( C-alpha) has 377 elements
Group 4 ( Backbone) has 1131 elements
Group 5 ( MainChain) has 1507 elements
Group 6 ( MainChain+Cb) has 1861 elements
Group 7 ( MainChain+H) has 1869 elements
Group 8 ( SideChain) has 4230 elements
Group 9 ( SideChain-H) has 1560 elements
Group 10 ( Prot-Masses) has 6099 elements
Group 11 ( non-Protein) has 64407 elements
Group 12 ( Other) has 64407 elements
Group 13 ( ZN2) has 1 elements
Group 14 ( UNK) has 46 elements
Group 15 ( SOD) has 60 elements
Group 16 ( CLA) has 64 elements
Group 17 ( TIP3) has 64236 elements
Group 18 ( lig) has 44 elements
Group 19 ( Protein_lig) has 6143 elements
Select a group: 14
Selected 14: 'UNK'
Back Off! I just backed up lig.pdb to ./#lig.pdb.10#
Segmentation fault (core dumped)Please, rebuild this file and make sure all groups are accesible and it's not corrupted
Ridwan20-alt
commented
1 year ago Sorry for the late response I will do that . Thank you
Ridwan20-alt
commented
1 year ago I have rebuilt the index file but still facing the segmentation error
marioernestovaldes
commented
1 year ago did you build it from scratch? can you send me the tpr file you are using?
Ridwan20-alt
commented
1 year ago Yes, I did
Ridwan20-alt
commented
1 year ago I'm trying to send it nut it's not supported to be sent through this medium
marioernestovaldes
commented
1 year ago try compressing it
Ridwan20-alt
commented
1 year ago marioernestovaldes
commented
1 year ago the trjectory you sent around has only 44 atoms... could you please check and send a trajectory containg at least the complex (I need only few frames for testing purposes)
Ridwan20-alt
commented
1 year ago can I send you the xtc file then ?
marioernestovaldes
commented
1 year ago yes please
Ridwan20-alt
commented
1 year ago Here is it: tpr2.zip
marioernestovaldes
commented
1 year ago Found the issue. When you generate the Protein_ligand group in the index_mod_gromacs.ndx you are leaving the ZN atom out and this leads to a numbering problem afterwards when generating the structure files. Please, make sure when generating the index_mod_gromacs.ndx:
0-create a new group for the receptor that will contain the Protein group (1) and the ZN2 atom (13) 1-create group for ligand without LPH particles 2-create a group called Protein_lig by merging the new receptor group and the ligand without LPH particle group
here are the commands:
gmx make_ndx -f step5_production.tpr -o index_mod_gromacs.ndx
:-) GROMACS - gmx make_ndx, 2021.3-bioconda (-:
GROMACS is written by:
Andrey Alekseenko Emile Apol Rossen Apostolov
Paul Bauer Herman J.C. Berendsen Par Bjelkmar
Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra
Gilles Gouaillardet Alan Gray Gerrit Groenhof
Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan
Dimitrios Karkoulis Peter Kasson Jiri Kraus
Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola
Szilard Pall Sander Pronk Roland Schulz
Michael Shirts Alexey Shvetsov Alfons Sijbers
Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx make_ndx, version 2021.3-bioconda
Executable: /media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/gmxMMPBSA_dev/bin.AVX2_256/gmx
Data prefix: /media/mario/92bb1dc0-1f5c-4566-bfea-709a64de54f8/mario/Programs/Installation/AmberTools20/amber20/miniconda/envs/gmxMMPBSA_dev
Working dir: /home/mario/Downloads/toppar1
Command line:
gmx make_ndx -f step5_production.tpr -o index_mod_gromacs.ndx
Reading structure file
Reading file step5_production.tpr, VERSION 2021.2 (single precision)
Reading file step5_production.tpr, VERSION 2021.2 (single precision)
Going to read 0 old index file(s)
Analysing residue names:
There are: 377 Protein residues
There are: 21538 Other residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
0 System : 70506 atoms
1 Protein : 6099 atoms
2 Protein-H : 3067 atoms
3 C-alpha : 377 atoms
4 Backbone : 1131 atoms
5 MainChain : 1507 atoms
6 MainChain+Cb : 1861 atoms
7 MainChain+H : 1869 atoms
8 SideChain : 4230 atoms
9 SideChain-H : 1560 atoms
10 Prot-Masses : 6099 atoms
11 non-Protein : 64407 atoms
12 Other : 64407 atoms
13 ZN2 : 1 atoms
14 UNK : 46 atoms
15 SOD : 60 atoms
16 CLA : 64 atoms
17 TIP3 : 64236 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> 1|13
Copied index group 1 'Protein'
Copied index group 13 'ZN2'
Merged two groups with OR: 6099 1 -> 6100
18 Protein_ZN2 : 6100 atoms
> name 18 receptor
> splitat 14
Splitting group 14 'UNK' into atoms
>
0 System : 70506 atoms
1 Protein : 6099 atoms
2 Protein-H : 3067 atoms
3 C-alpha : 377 atoms
4 Backbone : 1131 atoms
5 MainChain : 1507 atoms
6 MainChain+Cb : 1861 atoms
7 MainChain+H : 1869 atoms
8 SideChain : 4230 atoms
9 SideChain-H : 1560 atoms
10 Prot-Masses : 6099 atoms
11 non-Protein : 64407 atoms
12 Other : 64407 atoms
13 ZN2 : 1 atoms
14 UNK : 46 atoms
15 SOD : 60 atoms
16 CLA : 64 atoms
17 TIP3 : 64236 atoms
18 receptor : 6100 atoms
19 UNK_CL1_6101 : 1 atoms
20 UNK_CL2_6102 : 1 atoms
21 UNK_O1_6103 : 1 atoms
22 UNK_O2_6104 : 1 atoms
23 UNK_N1_6105 : 1 atoms
24 UNK_N2_6106 : 1 atoms
25 UNK_C1_6107 : 1 atoms
26 UNK_C2_6108 : 1 atoms
27 UNK_C3_6109 : 1 atoms
28 UNK_C4_6110 : 1 atoms
29 UNK_C5_6111 : 1 atoms
30 UNK_C6_6112 : 1 atoms
31 UNK_C7_6113 : 1 atoms
32 UNK_C8_6114 : 1 atoms
33 UNK_C9_6115 : 1 atoms
34 UNK_C10_6116 : 1 atoms
35 UNK_C11_6117 : 1 atoms
36 UNK_C12_6118 : 1 atoms
37 UNK_C13_6119 : 1 atoms
38 UNK_C14_6120 : 1 atoms
39 UNK_C15_6121 : 1 atoms
40 UNK_C16_6122 : 1 atoms
41 UNK_C17_6123 : 1 atoms
42 UNK_C18_6124 : 1 atoms
43 UNK_H1_6125 : 1 atoms
44 UNK_H2_6126 : 1 atoms
45 UNK_H3_6127 : 1 atoms
46 UNK_H4_6128 : 1 atoms
47 UNK_H5_6129 : 1 atoms
48 UNK_H6_6130 : 1 atoms
49 UNK_H7_6131 : 1 atoms
50 UNK_H8_6132 : 1 atoms
51 UNK_H9_6133 : 1 atoms
52 UNK_H10_6134 : 1 atoms
53 UNK_H11_6135 : 1 atoms
54 UNK_H12_6136 : 1 atoms
55 UNK_H13_6137 : 1 atoms
56 UNK_H14_6138 : 1 atoms
57 UNK_H15_6139 : 1 atoms
58 UNK_H16_6140 : 1 atoms
59 UNK_H17_6141 : 1 atoms
60 UNK_H18_6142 : 1 atoms
61 UNK_H19_6143 : 1 atoms
62 UNK_H20_6144 : 1 atoms
63 UNK_LP1_6145 : 1 atoms
64 UNK_LP2_6146 : 1 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> 63|64
Copied index group 63 'UNK_LP1_6145'
Copied index group 64 'UNK_LP2_6146'
Merged two groups with OR: 1 1 -> 2
65 UNK_LP1_6145_UNK_LP2_6146: 2 atoms
> 14&!65
Copied index group 14 'UNK'
Copied index group 65 'UNK_LP1_6145_UNK_LP2_6146'
Complemented group: 70504 atoms
Merged two groups with AND: 46 70504 -> 44
66 UNK_&_!UNK_LP1_6145_UNK_LP2_6146: 44 atoms
> del 19-65
Removed group 19 'UNK_CL1_6101'
Removed group 20 'UNK_CL2_6102'
Removed group 21 'UNK_O1_6103'
Removed group 22 'UNK_O2_6104'
Removed group 23 'UNK_N1_6105'
Removed group 24 'UNK_N2_6106'
Removed group 25 'UNK_C1_6107'
Removed group 26 'UNK_C2_6108'
Removed group 27 'UNK_C3_6109'
Removed group 28 'UNK_C4_6110'
Removed group 29 'UNK_C5_6111'
Removed group 30 'UNK_C6_6112'
Removed group 31 'UNK_C7_6113'
Removed group 32 'UNK_C8_6114'
Removed group 33 'UNK_C9_6115'
Removed group 34 'UNK_C10_6116'
Removed group 35 'UNK_C11_6117'
Removed group 36 'UNK_C12_6118'
Removed group 37 'UNK_C13_6119'
Removed group 38 'UNK_C14_6120'
Removed group 39 'UNK_C15_6121'
Removed group 40 'UNK_C16_6122'
Removed group 41 'UNK_C17_6123'
Removed group 42 'UNK_C18_6124'
Removed group 43 'UNK_H1_6125'
Removed group 44 'UNK_H2_6126'
Removed group 45 'UNK_H3_6127'
Removed group 46 'UNK_H4_6128'
Removed group 47 'UNK_H5_6129'
Removed group 48 'UNK_H6_6130'
Removed group 49 'UNK_H7_6131'
Removed group 50 'UNK_H8_6132'
Removed group 51 'UNK_H9_6133'
Removed group 52 'UNK_H10_6134'
Removed group 53 'UNK_H11_6135'
Removed group 54 'UNK_H12_6136'
Removed group 55 'UNK_H13_6137'
Removed group 56 'UNK_H14_6138'
Removed group 57 'UNK_H15_6139'
Removed group 58 'UNK_H16_6140'
Removed group 59 'UNK_H17_6141'
Removed group 60 'UNK_H18_6142'
Removed group 61 'UNK_H19_6143'
Removed group 62 'UNK_H20_6144'
Removed group 63 'UNK_LP1_6145'
Removed group 64 'UNK_LP2_6146'
Removed group 65 'UNK_LP1_6145_UNK_LP2_6146'
>
0 System : 70506 atoms
1 Protein : 6099 atoms
2 Protein-H : 3067 atoms
3 C-alpha : 377 atoms
4 Backbone : 1131 atoms
5 MainChain : 1507 atoms
6 MainChain+Cb : 1861 atoms
7 MainChain+H : 1869 atoms
8 SideChain : 4230 atoms
9 SideChain-H : 1560 atoms
10 Prot-Masses : 6099 atoms
11 non-Protein : 64407 atoms
12 Other : 64407 atoms
13 ZN2 : 1 atoms
14 UNK : 46 atoms
15 SOD : 60 atoms
16 CLA : 64 atoms
17 TIP3 : 64236 atoms
18 receptor : 6100 atoms
19 UNK_&_!UNK_LP1_6145_UNK_LP2_6146: 44 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> name 19 ligand
> 18|19
Copied index group 18 'receptor'
Copied index group 19 'ligand'
Merged two groups with OR: 6100 44 -> 6144
20 receptor_ligand : 6144 atoms
> name 20 complex
>
0 System : 70506 atoms
1 Protein : 6099 atoms
2 Protein-H : 3067 atoms
3 C-alpha : 377 atoms
4 Backbone : 1131 atoms
5 MainChain : 1507 atoms
6 MainChain+Cb : 1861 atoms
7 MainChain+H : 1869 atoms
8 SideChain : 4230 atoms
9 SideChain-H : 1560 atoms
10 Prot-Masses : 6099 atoms
11 non-Protein : 64407 atoms
12 Other : 64407 atoms
13 ZN2 : 1 atoms
14 UNK : 46 atoms
15 SOD : 60 atoms
16 CLA : 64 atoms
17 TIP3 : 64236 atoms
18 receptor : 6100 atoms
19 ligand : 44 atoms
20 complex : 6144 atoms
nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups
'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues
't': atom type '|': or 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
'ri': residue index
> q
Back Off! I just backed up index_mod_gromacs.ndx to ./#index_mod_gromacs.ndx.3#
GROMACS reminds you: "If my PhD doesn't allow me to be right on the internet, what is it even good for?" (Martin Vögele)echo 20 | gmx trjconv -s step5_production.tpr -f output.xtc -dump 0 -o str_noLP.pdb -n index_mod_gromacs.ndx
echo 20 | gmx trjconv -s step5_production.tpr -f output.xtc -o com_traj.xtc -n index_mod_gromacs.ndx
gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index_mod_gromacs.ndx -cg 18 19 -ct com_traj.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csvThank you so much. It works now after considering the zinc atom.
I have a question , and I will be glad if you could be of help in answering it . I noticed that for various complexes I'm studying when I analyze a large portion of the frames say between 500( start) to 1000 (end), I do get a positive delta total value, however, if I choose to analyze only a small portion of my trajectory for BFE calculations say between 1(start) to 4 or 5(end) frame, I get a negative delta total value. Due to this observation I was wondering if there is a relationship between the range of frames selected in the .in file and final delta total expected after the binding free energy calculations. I will be glad if you can enlighten me on this.
Thanks, Ridwan
marioernestovaldes
commented
1 year ago Typically 500-1000 frames are ok for the stats... Since you are using PB, the EDISPER term probably has a high positive contribution. Try using inp=1 with PB and see how it goes...
More info here (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions_2)
Ridwan20-alt
commented
1 year ago Thanks for your suggestions. I have tried to use inp=1 but still there is no difference as I still obtain positive delta total value(2.85) for a large range of frames(1 to 100), and a moderately low negative(-2.06)value for a small range of frame (1-3 frames).
marioernestovaldes
commented
1 year ago Try increasing the internal dielectric constant...
Ridwan20-alt
commented
1 year ago [INFO ] Running calculations on normal system... [INFO ] Beginning PB calculations with /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander [INFO ] calculating complex contribution... 0%| | 0/20 [elapsed: 00:00 remaining: ?]At line 143 of file /tmp/ebuser/avx2/AmberTools/21/foss-2020a/amber20_src/AmberTools/src/sander/rgroup.F90 (unit = 5, file = '_GMXMMPBSA_pb_decomp_com.mdin') Fortran runtime error: End of file
Error termination. Backtrace:
[ERROR ] CalcError /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21/bin/sander failed with prmtop COM.prmtop!
If you are using sander and PB calculation, check the *.mdout files to get the sander error
.
Check the gmx_MMPBSA.log file to report the problem.
File "/home/oladayo/venv_gmxMMPBSA/bin/gmx_MMPBSA", line 8, in
If you are using sander and PB calculation, check the *.mdout files to get the sander error
Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.
marioernestovaldes
commented
1 year ago This is a bug... let's move it to a new issue and close this one
marioernestovaldes
commented
1 year ago The issue has been fixed... please update gmx_MMPBSA as follows:
python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U
please, post any error related to this issue in #352
Bug summary
Hi I am trying to calculate the mmpbsa between a protein and a ligand with LPH atoms. After following this tutorial(https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/examples/Protein_ligand_LPH_atoms_CHARMMff) to prepare my input files I use the following command: gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 18 -ct com_traj.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv However, it gives me this error and the job stops after a few minutes: [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 1_18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [ERROR ] MMPBSA_Error /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf failed when querying com_traj.xtc. Check the gmx_MMPBSA.log file to report the problem. File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa app.make_prmtops() File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/main.py", line 533, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology self.gmx2pdb() File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/make_top.py", line 232, in gmx2pdb GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0])) File "/scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/lib/python3.8/site-packages/GMXMMPBSA/exceptions.py", line 169, in init raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.') MMPBSA_Error: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf failed when querying com_traj.xtc Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.
I will be glad to see you guide me on how to get this resolved .
Regards, Ridwan
Terminal output
gmx_MMPBSA.log
[INFO ] Starting gmx_MMPBSA v1.5.0.3 [DEBUG ] WDIR : /scratch/oladayo/Dynamics/LIG2/L32/L32 [DEBUG ] AMBERHOME : /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/ambertools/21 [DEBUG ] PYTHON EXE : /scratch/oladayo/Dynamics/LIG2/L32/L32/venv_gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.8.10 (default, Jun 16 2021, 14:20:20) [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+5.g16fb2364 [DEBUG ] OS PLATFORM : Linux-3.10.0-1160.80.1.el7.x86_64-x86_64-with-glibc2.2.5 [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 str_noLP.pdb -ci index_mod_gromacs.ndx -cg 1 18 -ct com_traj.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |Sample input file for PB calculation [DEBUG ] |This input file is meant to show only that gmx_MMPBSA works. Although, we tried to use the input files as recommended [DEBUG ] |in the Amber manual, some parameters have been changed to perform more expensive calculations in a reasonable amount of time. Feel free to change the [DEBUG ] |parameters according to what is better for your system. [DEBUG ] | [DEBUG ] |&general [DEBUG ] |sys_name="Prot-Lig-CHARMM", [DEBUG ] |startframe=5, [DEBUG ] |endframe=9, [DEBUG ] |# In gmx_MMPBSA v1.5.0 we have added a new PB radii set named charmm_radii. This radii set should be used only [DEBUG ] |# with systems prepared with CHARMM force fields. Uncomment the line below to use charmm_radii set [DEBUG ] |#PBRadii=7, [DEBUG ] |/ [DEBUG ] |&pb [DEBUG ] |# radiopt=0 is recommended which means using radii from the prmtop file for both the PB calculation and for the NP [DEBUG ] |# calculation [DEBUG ] |istrng=0.15, fillratio=4.0, radiopt=0 [DEBUG ] |/-------------------------------------------------------------- [DEBUG ] [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/2021.4/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 name 1 GMXMMPBSA_REC\n name 18 GMXMMPBSA_LIG\n 1 | 18\n q\n | /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx make_ndx -n index_mod_gromacs.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx make_ndx, 2021.4 (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx make_ndx, version 2021.4 [DEBUG ] Executable: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx [DEBUG ] Data prefix: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4 [DEBUG ] Working dir: /scratch/oladayo/Dynamics/LIG2/L32/L32 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n index_mod_gromacs.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "I was taught that the way of progress was neither swift nor easy." (Marie Curie) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] Counted atom numbers up to 70506 in index file [DEBUG ] [DEBUG ] 0 System : 70506 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 : 64407 atoms [DEBUG ] 12 Other : 64407 atoms [DEBUG ] 13 ZN2 : 1 atoms [DEBUG ] 14 UNK : 46 atoms [DEBUG ] 15 SOD : 60 atoms [DEBUG ] 16 CLA : 64 atoms [DEBUG ] 17 TIP3 : 64236 atoms [DEBUG ] 18 lig : 44 atoms [DEBUG ] 19 Protein_lig : 6143 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 1 'GMXMMPBSA_REC' [DEBUG ] Copied index group 18 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 6099 44 -> 6143 [DEBUG ] [DEBUG ] 20 GMXMMPBSA_REC_GMXMMPBSA_LIG: 6143 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group 1_18 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb [ERROR ] MMPBSA_Error /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/MPI/gcc9/openmpi4/gromacs/2021.4/bin/gmx editconf failed when querying com_traj.xtc. Check the gmx_MMPBSA.log file to report the problem.
Operating system
No response
gmx_MMPBSA Version
No response
Python version
No response
Installation
None