but when I launch mmgbsa I have met this problem : bin/gmx editconf failed when querying com_traj.xtc.

[Valdes-Tresanco-MS]

          but when I launch mmgbsa I have met this problem : bin/gmx editconf failed when querying com_traj.xtc.
       Check the gmx_MMPBSA.log file to report the problem.

_Originally posted by @AbdelmoujoudFaris in https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/153#issuecomment-1535602792_

[Valdes-Tresanco-MS]

Please, open a new issue to report any error, since is easier to track. Please, attach/upload the gmx_MMPBSA.log file

[AbdelmoujoudFaris]

here's the log file in this link https://github.com/AbdelmoujoudFaris/mmgbsa1/blob/main/mmgbsalog

[Valdes-Tresanco-MS]

Probably, the problem here is you are using a PDB file as the structure, which does not contain the same number of atoms as the index.ndx. Please, try using a tpr file instead of pdb.

PS: You can upload files to this issue specifically. If the format is not allowed, only change the extension.

[AbdelmoujoudFaris]

log: [INFO ] Starting gmx_MMPBSA v1.6.0 [DEBUG ] WDIR : /home/a.alix/Redynamicarti2/5/gromacs/gmxx [DEBUG ] AMBERHOME : /home/a.alix/.conda/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/a.alix/.conda/envs/gmxMMPBSA/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 : /home/a.alix/.conda/envs/gmxMMPBSA/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 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="Protein_lig", [DEBUG ] |startframe=5, [DEBUG ] |endframe=50, [DEBUG ] |forcefields="oldff/leaprc.ff99SB",leaprc.gaff" [DEBUG ] |/ [DEBUG ] |&gb [DEBUG ] |igb=5, saltcon=0.150, [DEBUG ] |/ [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 17 GMXMMPBSA_LIG\n 1 | 17\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 str_noLP.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/gmxx [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 ] ------------------------------------------------------- [DEBUG ] Program: gmx make_ndx, version 2021.3-EasyBuild-4.5.2 [DEBUG ] Source file: src/gromacs/tools/make_ndx.cpp (line 1204) [DEBUG ] [DEBUG ] Fatal error: [DEBUG ] Error reading user input [DEBUG ] [DEBUG ] For more information and tips for troubleshooting, please check the GROMACS [DEBUG ] website at http://www.gromacs.org/Documentation/Errors [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 17 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 4349 52707 -> 57056 [DEBUG ] [DEBUG ] 19 GMXMMPBSA_REC_GMXMMPBSA_LIG: 57056 atoms [DEBUG ] [DEBUG ] > [DEBUG ] [DEBUG ] 0 System : 57264 atoms [DEBUG ] 1 GMXMMPBSA_REC : 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 GMXMMPBSA_LIG : 52707 atoms [DEBUG ] 18 Protein_lig : 4405 atoms [DEBUG ] 19 GMXMMPBSA_REC_GMXMMPBSA_LIG: 57056 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 ] > [ERROR ] MMPBSA_Error /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/bin/gmx make_ndx failed when querying index_mod_gromacs.ndx. Check the gmx_MMPBSA.log file to report the problem.

[AbdelmoujoudFaris]

slurm out: [INFO ] Starting gmx_MMPBSA v1.6.0 [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

[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... [ERROR ] MMPBSA_Error /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/bin/gmx make_ndx failed when querying index_mod_gromacs.ndx. Check the gmx_MMPBSA.log file to report the problem. File "/home/a.alix/.conda/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 10, in sys.exit(gmxmmpbsa()) File "/home/a.alix/.local/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/home/a.alix/.local/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 689, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/home/a.alix/.local/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology self.gmx2pdb() File "/home/a.alix/.local/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 263, in gmx2pdb GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(self.make_ndx), self.FILES.complex_index)) File "/home/a.alix/.local/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in init raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.') MMPBSA_Error: /cm/shared/apps/eb/software/GROMACS/2021.3-foss-2021a/bin/gmx make_ndx failed when querying index_mod_gromacs.ndx Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained. [1683281374.285894] [data36:1415793:0] ib_md.c:1161 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued. [1683281374.286448] [data36:1415793:0] ib_md.c:1162 UCX WARN IB: data corruption might occur when using registered memory. [1683281374.376486] [data36:1415793:0] ib_md.c:1161 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued. [1683281374.376496] [data36:1415793:0] ib_md.c:1162 UCX WARN IB: data corruption might occur when using registered memory. [1683281374.452471] [data36:1415793:0] ib_md.c:1161 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued. [1683281374.452480] [data36:1415793:0] ib_md.c:1162 UCX WARN IB: data corruption might occur when using registered memory.

[AbdelmoujoudFaris]

i have made mmgbsa succesfly for other complexes out files md , but for this I can't do it,

[AbdelmoujoudFaris]

0 System : 57264 atoms 1 Protein : 4349 atoms 2 Protein-H : 2176 atoms 3 C-alpha : 271 atoms 4 Backbone : 813 atoms 5 MainChain : 1083 atoms 6 MainChain+Cb : 1339 atoms 7 MainChain+H : 1338 atoms 8 SideChain : 3011 atoms 9 SideChain-H : 1093 atoms 10 Prot-Masses : 4349 atoms 11 non-Protein : 52915 atoms 12 Other : 52915 atoms 13 PTR : 50 atoms 14 LIG : 56 atoms 15 SOD : 52 atoms 16 CLA : 50 atoms 17 TIP3 : 52707 atoms

[Valdes-Tresanco-MS]

Please, send me your files (tpr, ndx, 5frames xtc, top, it's and the toppar)

[AbdelmoujoudFaris]

New folder - 1.zip Okay, here are the files you need and thank you

[Valdes-Tresanco-MS]

Please, attach the toppar folder

[AbdelmoujoudFaris]

toppar.zip

[Valdes-Tresanco-MS]

I don't get any errors, but I see suspicious things. In the index, LIG appears in group 14, while PTR appears in group 13, which I'm not sure what it is. In one of your outputs, you seem to be carrying out the procedure for ligands with LPH but it doesn't seem to be the case with the system you sent me. As I also see, the ligand has a carbanion, is it due to a bad procedure to eliminate the LPH? I this system the correct one?

[AbdelmoujoudFaris]

for the systems without LPH I have already made the same procedure it works well without touching the files in toppar, but for this case also I noted that LIG in 14

[Valdes-Tresanco-MS]

I think I'm lost. Which system is not working? Please send those files (include all necessary files in a zip). Make sure you are sending the ones that have problems

[Valdes-Tresanco-MS]

@AbdelmoujoudFaris Did you solve the problem?

[AbdelmoujoudFaris]

Hello dear Valdes-Tresanco, yes I did it by merging proteins with PTR and deleting single PTR.