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mmgbsalog
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[INFO ] Starting gmx_MMPBSA v1.6.0
[DEBUG ] WDIR : /home/a.alix/Redynamicarti2/5/gromacs/gx
[DEBUG ] AMBERHOME : /home/a.alix/.conda/envs/gmxMMPBSA
[DEBUG ] PYTHON EXE : /data/shared/apps2/EasyBuild/software/Python/3.9.5-GCCcore-10.3.0/bin/python
[DEBUG ] PYTHON VERSION: 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0]
[DEBUG ] MPI : /cm/shared/apps/eb/software/OpenMPI/4.1.1-GCC-10.3.0/bin/mpirun
[DEBUG ] ParmEd : 3.4.4
[DEBUG ] OS PLATFORM : Linux-4.18.0-348.12.2.el8_5.x86_64-x86_64-with-glibc2.28
[DEBUG ] OS SYSTEM : Linux
[DEBUG ] OS VERSION : #1 SMP Mon Jan 17 07:06:06 EST 2022
[DEBUG ] OS PROCESSOR : x86_64
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs com.pdb -ci index_mod_gromacs.ndx -cg 1 14 -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=1,
[DEBUG ] |endframe=10,
[DEBUG ] |/
[DEBUG ] |&gb
[DEBUG ] |igb=5, saltcon=0.150,
[DEBUG ] |/
[DEBUG ] |--------------------------------------------------------------
[DEBUG ]
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/a.alix/.conda/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/a.alix/.conda/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/a.alix/.conda/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/a.alix/.conda/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/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 14 GMXMMPBSA_LIG\n 1 | 14\n q\n" | /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/bin/gmx make_ndx -n index_mod_gromacs.ndx -o _GMXMMPBSA_COM_index.ndx -f com.pdb
[DEBUG ] :-) GROMACS - gmx make_ndx, 2021.3-EasyBuild-4.5.2 (-:
[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 2021.3-EasyBuild-4.5.2
[DEBUG ] Executable: /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/bin/gmx
[DEBUG ] Data prefix: /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a
[DEBUG ] Working dir: /home/a.alix/Redynamicarti2/5/gromacs/gx
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index_mod_gromacs.ndx -o _GMXMMPBSA_COM_index.ndx -f com.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ]
[DEBUG ] GROMACS reminds you: "I Had So Many Problem, and Then I Got Me a Walkman" (F. Black)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 57264 atoms
[DEBUG ] 1 Protein : 4349 atoms
[DEBUG ] 2 Protein-H : 2176 atoms
[DEBUG ] 3 C-alpha : 271 atoms
[DEBUG ] 4 Backbone : 813 atoms
[DEBUG ] 5 MainChain : 1083 atoms
[DEBUG ] 6 MainChain+Cb : 1339 atoms
[DEBUG ] 7 MainChain+H : 1338 atoms
[DEBUG ] 8 SideChain : 3011 atoms
[DEBUG ] 9 SideChain-H : 1093 atoms
[DEBUG ] 10 Prot-Masses : 4349 atoms
[DEBUG ] 11 non-Protein : 52915 atoms
[DEBUG ] 12 Other : 52915 atoms
[DEBUG ] 13 PTR : 50 atoms
[DEBUG ] 14 LIG : 56 atoms
[DEBUG ] 15 SOD : 52 atoms
[DEBUG ] 16 CLA : 50 atoms
[DEBUG ] 17 TIP3 : 52707 atoms
[DEBUG ] 18 Protein_LIG : 4405 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 14 'GMXMMPBSA_LIG'
[DEBUG ] Merged two groups with OR: 4349 56 -> 4405
[DEBUG ]
[DEBUG ] 19 GMXMMPBSA_REC_GMXMMPBSA_LIG: 4405 atoms
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group Protein_LIG (1_14) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/bin/gmx editconf -f com.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG ] :-) GROMACS - gmx editconf, 2021.3-EasyBuild-4.5.2 (-:
[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 2021.3-EasyBuild-4.5.2
[DEBUG ] Executable: /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/bin/gmx
[DEBUG ] Data prefix: /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a
[DEBUG ] Working dir: /home/a.alix/Redynamicarti2/5/gromacs/gx
[DEBUG ] Command line:
[DEBUG ] gmx editconf -f com.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Select a group for output:
[DEBUG ] Group 0 ( System) has 57264 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 4349 elements
[DEBUG ] Group 2 ( Protein-H) has 2176 elements
[DEBUG ] Group 3 ( C-alpha) has 271 elements
[DEBUG ] Group 4 ( Backbone) has 813 elements
[DEBUG ] Group 5 ( MainChain) has 1083 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1339 elements
[DEBUG ] Group 7 ( MainChain+H) has 1338 elements
[DEBUG ] Group 8 ( SideChain) has 3011 elements
[DEBUG ] Group 9 ( SideChain-H) has 1093 elements
[DEBUG ] Group 10 ( Prot-Masses) has 4349 elements
[DEBUG ] Group 11 ( non-Protein) has 52915 elements
[DEBUG ] Group 12 ( Other) has 52915 elements
[DEBUG ] Group 13 ( PTR) has 50 elements
[DEBUG ] Group 14 ( GMXMMPBSA_LIG) has 56 elements
[DEBUG ] Group 15 ( SOD) has 52 elements
[DEBUG ] Group 16 ( CLA) has 50 elements
[DEBUG ] Group 17 ( TIP3) has 52707 elements
[DEBUG ] Group 18 ( Protein_LIG) has 4405 elements
[DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4405 elements
[DEBUG ] Select a group:
[ERROR ] MMPBSA_Error /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/bin/gmx editconf failed when querying com_traj.xtc.
Check the gmx_MMPBSA.log file to report the problem.