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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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[Bug-gmx_MMPBSA]: Alanine scanning #298

Closed aptamer1234 closed 1 year ago

aptamer1234 commented 1 year ago

Bug summary

I use the alanine scanning program in the example, but the ligands and receptors cannot be recognized. Do I need to create the PDB files of the ligands and receptors by myself?

Terminal output

[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 21: 'GMXMMPBSA_LIG'
[INFO   ] Checking the structures consistency...
[INFO   ] 
[INFO   ] Generating AMBER Compatible PDB Files...
[INFO   ] Changing the Complex residues name format from GROMACS to AMBER...
[INFO   ] Changing the Receptor residues name format from GROMACS to AMBER...
[INFO   ] Changing the Ligand residues name format from GROMACS to AMBER...
[INFO   ] Splitting  receptor and ligand in PDB files..
[ERROR  ] MMPBSA_Error For decomposition analysis, you most define residues for both receptor and ligand!.
           Check the gmx_MMPBSA.log file to report the problem.

gmx_MMPBSA.log

[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 21: 'GMXMMPBSA_LIG' [INFO ] Checking the structures consistency... [INFO ] [INFO ] Generating AMBER Compatible PDB Files... [INFO ] Changing the Complex residues name format from GROMACS to AMBER... [INFO ] Changing the Receptor residues name format from GROMACS to AMBER... [INFO ] Changing the Ligand residues name format from GROMACS to AMBER... [INFO ] Splitting receptor and ligand in PDB files.. [ERROR ] MMPBSA_Error For decomposition analysis, you most define residues for both receptor and ligand!. Check the gmx_MMPBSA.log file to report the problem.

Operating system

Ubuntu22.04

gmx_MMPBSA Version

gmx_MMPBSA_test v1.5.6+30.g0c3c6ec based on MMPBSA version 16.0

Python version

python 3.9

Installation

from source (.tar.gz)

marioernestovaldes commented 1 year ago

Seems like the groups defined don't contain the right atoms. could you please attach the .log file?

aptamer1234 commented 1 year ago

[INFO ] Starting gmx_MMPBSA v1.5.6+30.g0c3c6ec [DEBUG ] WDIR : /media/b1612/0b343021-fe7b-40e9-999b-fdf4f587092d/scFv-pp/gmx_MMPBSA_test/examples/Alanine_scanning [DEBUG ] AMBERHOME : /home/b1612/miniconda3/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/b1612/miniconda3/envs/gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:56:21) [GCC 10.3.0] [DEBUG ] MPI : /home/b1612/miniconda3/envs/gmxMMPBSA/bin/mpirun [DEBUG ] ParmEd : 3.4.3+10.ga195c7e [DEBUG ] OS PLATFORM : Linux-5.15.0-52-generic-x86_64-with-glibc2.35 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #58-Ubuntu SMP Thu Oct 13 08:03:55 UTC 2022 [DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 21 -ct com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |Sample input file for Alanine scanning [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="Alanine_Scanning", [DEBUG ] |startframe=1, [DEBUG ] |endframe=10, [DEBUG ] |forcefields="leaprc.protein.ff14SB", [DEBUG ] |PBRadii=4, [DEBUG ] |/ [DEBUG ] |&gb [DEBUG ] |igb=8, saltcon=0.150, [DEBUG ] |/ [DEBUG ] |&alanine_scanning [DEBUG ] |mutant='ALA', mutant_res='A:23', cas_intdiel=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 /home/b1612/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/b1612/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/b1612/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/b1612/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/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 20 GMXMMPBSA_REC\n name 21 GMXMMPBSA_LIG\n 20 | 21\n q\n | /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx make_ndx, 2021.3-bioconda (-: [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-bioconda [DEBUG ] Executable: /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/b1612/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /media/b1612/0b343021-fe7b-40e9-999b-fdf4f587092d/scFv-pp/gmx_MMPBSA_test/examples/Alanine_scanning [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "There is no reason for any individual to have a computer in his home." (Ken Olsen, head of Digital Equipment Corp.) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] Counted atom numbers up to 11480 in index file [DEBUG ] [DEBUG ] 0 System : 11480 atoms [DEBUG ] 1 Protein : 608 atoms [DEBUG ] 2 Protein-H : 319 atoms [DEBUG ] 3 C-alpha : 39 atoms [DEBUG ] 4 Backbone : 117 atoms [DEBUG ] 5 MainChain : 158 atoms [DEBUG ] 6 MainChain+Cb : 194 atoms [DEBUG ] 7 MainChain+H : 196 atoms [DEBUG ] 8 SideChain : 412 atoms [DEBUG ] 9 SideChain-H : 161 atoms [DEBUG ] 10 Prot-Masses : 608 atoms [DEBUG ] 11 non-Protein : 10872 atoms [DEBUG ] 12 Ion : 21 atoms [DEBUG ] 13 Na+ : 11 atoms [DEBUG ] 14 Cl- : 10 atoms [DEBUG ] 15 TP3 : 10851 atoms [DEBUG ] 16 Other : 10851 atoms [DEBUG ] 17 Na+ : 11 atoms [DEBUG ] 18 Cl- : 10 atoms [DEBUG ] 19 TP3 : 10851 atoms [DEBUG ] 20 Protein_chain1 : 478 atoms [DEBUG ] 21 Protein_chain2 : 130 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 20 'GMXMMPBSA_REC' [DEBUG ] Copied index group 21 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 478 130 -> 608 [DEBUG ] [DEBUG ] 22 GMXMMPBSA_REC_GMXMMPBSA_LIG: 608 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group 20_21 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-: [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 trjconv, version 2021.3-bioconda [DEBUG ] Executable: /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/b1612/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /media/b1612/0b343021-fe7b-40e9-999b-fdf4f587092d/scFv-pp/gmx_MMPBSA_test/examples/Alanine_scanning [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2018.3 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2018.3 (single precision) [DEBUG ] Group 0 ( System) has 11480 elements [DEBUG ] Group 1 ( Protein) has 608 elements [DEBUG ] Group 2 ( Protein-H) has 319 elements [DEBUG ] Group 3 ( C-alpha) has 39 elements [DEBUG ] Group 4 ( Backbone) has 117 elements [DEBUG ] Group 5 ( MainChain) has 158 elements [DEBUG ] Group 6 ( MainChain+Cb) has 194 elements [DEBUG ] Group 7 ( MainChain+H) has 196 elements [DEBUG ] Group 8 ( SideChain) has 412 elements [DEBUG ] Group 9 ( SideChain-H) has 161 elements [DEBUG ] Group 10 ( Prot-Masses) has 608 elements [DEBUG ] Group 11 ( non-Protein) has 10872 elements [DEBUG ] Group 12 ( Ion) has 21 elements [DEBUG ] Group 13 ( Na+) has 11 elements [DEBUG ] Group 14 ( Cl-) has 10 elements [DEBUG ] Group 15 ( TP3) has 10851 elements [DEBUG ] Group 16 ( Other) has 10851 elements [DEBUG ] Group 17 ( Na+) has 11 elements [DEBUG ] Group 18 ( Cl-) has 10 elements [DEBUG ] Group 19 ( TP3) has 10851 elements [DEBUG ] Group 20 ( GMXMMPBSA_REC) has 478 elements [DEBUG ] Group 21 ( GMXMMPBSA_LIG) has 130 elements [DEBUG ] Group 22 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 608 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of com_traj.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 1.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "There is no reason for any individual to have a computer in his home." (Ken Olsen, head of Digital Equipment Corp.) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 22: '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 20 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo 20 | /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-: [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 trjconv, version 2021.3-bioconda [DEBUG ] Executable: /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/b1612/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /media/b1612/0b343021-fe7b-40e9-999b-fdf4f587092d/scFv-pp/gmx_MMPBSA_test/examples/Alanine_scanning [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2018.3 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2018.3 (single precision) [DEBUG ] Group 0 ( System) has 11480 elements [DEBUG ] Group 1 ( Protein) has 608 elements [DEBUG ] Group 2 ( Protein-H) has 319 elements [DEBUG ] Group 3 ( C-alpha) has 39 elements [DEBUG ] Group 4 ( Backbone) has 117 elements [DEBUG ] Group 5 ( MainChain) has 158 elements [DEBUG ] Group 6 ( MainChain+Cb) has 194 elements [DEBUG ] Group 7 ( MainChain+H) has 196 elements [DEBUG ] Group 8 ( SideChain) has 412 elements [DEBUG ] Group 9 ( SideChain-H) has 161 elements [DEBUG ] Group 10 ( Prot-Masses) has 608 elements [DEBUG ] Group 11 ( non-Protein) has 10872 elements [DEBUG ] Group 12 ( Ion) has 21 elements [DEBUG ] Group 13 ( Na+) has 11 elements [DEBUG ] Group 14 ( Cl-) has 10 elements [DEBUG ] Group 15 ( TP3) has 10851 elements [DEBUG ] Group 16 ( Other) has 10851 elements [DEBUG ] Group 17 ( Na+) has 11 elements [DEBUG ] Group 18 ( Cl-) has 10 elements [DEBUG ] Group 19 ( TP3) has 10851 elements [DEBUG ] Group 20 ( GMXMMPBSA_REC) has 478 elements [DEBUG ] Group 21 ( GMXMMPBSA_LIG) has 130 elements [DEBUG ] Group 22 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 608 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of com_traj.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 1.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "There is no reason for any individual to have a computer in his home." (Ken Olsen, head of Digital Equipment Corp.) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 20: '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 21 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo 21 | /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-: [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 trjconv, version 2021.3-bioconda [DEBUG ] Executable: /home/b1612/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/b1612/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /media/b1612/0b343021-fe7b-40e9-999b-fdf4f587092d/scFv-pp/gmx_MMPBSA_test/examples/Alanine_scanning [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2018.3 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2018.3 (single precision) [DEBUG ] Group 0 ( System) has 11480 elements [DEBUG ] Group 1 ( Protein) has 608 elements [DEBUG ] Group 2 ( Protein-H) has 319 elements [DEBUG ] Group 3 ( C-alpha) has 39 elements [DEBUG ] Group 4 ( Backbone) has 117 elements [DEBUG ] Group 5 ( MainChain) has 158 elements [DEBUG ] Group 6 ( MainChain+Cb) has 194 elements [DEBUG ] Group 7 ( MainChain+H) has 196 elements [DEBUG ] Group 8 ( SideChain) has 412 elements [DEBUG ] Group 9 ( SideChain-H) has 161 elements [DEBUG ] Group 10 ( Prot-Masses) has 608 elements [DEBUG ] Group 11 ( non-Protein) has 10872 elements [DEBUG ] Group 12 ( Ion) has 21 elements [DEBUG ] Group 13 ( Na+) has 11 elements [DEBUG ] Group 14 ( Cl-) has 10 elements [DEBUG ] Group 15 ( TP3) has 10851 elements [DEBUG ] Group 16 ( Other) has 10851 elements [DEBUG ] Group 17 ( Na+) has 11 elements [DEBUG ] Group 18 ( Cl-) has 10 elements [DEBUG ] Group 19 ( TP3) has 10851 elements [DEBUG ] Group 20 ( GMXMMPBSA_REC) has 478 elements [DEBUG ] Group 21 ( GMXMMPBSA_LIG) has 130 elements [DEBUG ] Group 22 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 608 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of com_traj.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 1.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "There is no reason for any individual to have a computer in his home." (Ken Olsen, head of Digital Equipment Corp.) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 21: 'GMXMMPBSA_LIG' [INFO ] Checking the structures consistency... [INFO ] [INFO ] Generating AMBER Compatible PDB Files... [INFO ] Changing the Complex residues name format from GROMACS to AMBER... [INFO ] Changing the Receptor residues name format from GROMACS to AMBER... [INFO ] Changing the Ligand residues name format from GROMACS to AMBER... [INFO ] Splitting receptor and ligand in PDB files.. [ERROR ] MMPBSA_Error For decomposition analysis, you most define residues for both receptor and ligand!. Check the gmx_MMPBSA.log file to report the problem.

marioernestovaldes commented 1 year ago

It's weird that it's throwing a decomposition error when you try to perform an alanine scanning... could you please send the files you're using to see what's going wrong?

aptamer1234 commented 1 year ago

It's weird that it's throwing a decomposition error when you try to perform an alanine scanning... could you please send the files you're using to see what's going wrong?

I‘m using the file from the example， https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/tree/master/examples/Alanine_scanning the command-line: gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 19 20 -ct com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

marioernestovaldes commented 1 year ago

If you are using the files from the alanine scanning tutorial please update gmxMMPBSA AS follows:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U

and run this command line:

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 21 -ct com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

and see if you get any errors...

aptamer1234 commented 1 year ago

If you are using the files from the alanine scanning tutorial please update gmxMMPBSA AS follows:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U

and run this command line:

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 21 -ct com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

and see if you get any errors...

Thank you very much, I'll try it again

aptamer1234 commented 1 year ago

If you are using the files from the alanine scanning tutorial please update gmxMMPBSA AS follows:

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA -U

and run this command line:

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 21 -ct com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

and see if you get any errors...

when I update gmxMMPBSA,I get an error as follows: Successfully built gmx-MMPBSA Failed to build mpi4py ERROR: Could not build wheels for mpi4py which use PEP 517 and cannot be installed directly

And the Alanine scanning also get the same error

marioernestovaldes commented 1 year ago

Try this command

gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 20 21 -ct com_traj.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

Valdes-Tresanco-MS commented 1 year ago

I broke the selection method fixing it for the decomposition :'(. However, I fixed it already (v1.5.6+33.ga66c23a7). Try to install it from GitHub 

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.git -U
aptamer1234 commented 1 year ago

image When I update gmxMMPBSA,I get an error.Will this affect the calculation result? If I ignore this error and continue to run the Alanine scanning, I still get the previous error

Valdes-Tresanco-MS commented 1 year ago

Please follow the instructions in the documentation to create an isolated conda environment (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/installation/#installing-gmx_mmpbsa-v15x). The problem here is that mpi4py is being installed with pip which usually ends in error. For this, it is better to install it from conda. Then install gmx_MMPBSA from Github as discussed above.

aptamer1234 commented 1 year ago

Please follow the instructions in the documentation to create an isolated conda environment (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/installation/#installing-gmx_mmpbsa-v15x). The problem here is that mpi4py is being installed with pip which usually ends in error. For this, it is better to install it from conda. Then install gmx_MMPBSA from Github as discussed above.

Thanks for your reply! I will try to install again