gmx editconf failed when querying com_traj.xtc #391

afwer1231 · 2023-07-05T09:38:52Z

afwer1231
Jul 5, 2023

dear Valdes:
I am trying to calculate the mmpbsa between a cyclodextrin 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:
mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index.ndx -cg 7 3 -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 :
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.

[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/ai/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/ai/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/ai/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/ai/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/bin/gmx
[INFO ] Checking external programs...Done.

[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group ligand_receptor (7_3) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error

/usr/bin/gmx editconf failed when querying com_traj.xtc

Check the gmx_MMPBSA.log file to report the problem.
tets
File "/home/ai/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in
sys.exit(gmxmmpbsa())
File "/home/ai/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
app.make_prmtops()
File "/home/ai/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/home/ai/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology
self.gmx2pdb()
File "/home/ai/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 289, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/home/ai/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in init
raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error:

/usr/bin/gmx editconf failed when querying com_traj.xtc

Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

I will be glad to see you guide me on how to get this resolved .

Regards,
fengwei ai

gmx_MMPBSA.log

[INFO ] Starting gmx_MMPBSA v1.6.1
[DEBUG ] WDIR : /home/ai/rmcd12-3dfnb(charm36)-gmxMMPDSA分析
[DEBUG ] AMBERHOME : /home/ai/miniconda3/envs/gmxMMPBSA
[DEBUG ] PYTHON EXE : /home/ai/miniconda3/envs/gmxMMPBSA/bin/python
[DEBUG ] PYTHON VERSION: 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:25:59) [GCC 10.3.0]
[DEBUG ] MPI : /home/ai/miniconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG ] ParmEd : 3.4.3
[DEBUG ] OS PLATFORM : Linux-5.15.90.1-microsoft-standard-WSL2-x86_64-with-glibc2.31
[DEBUG ] OS SYSTEM : Linux
[DEBUG ] OS VERSION : #1 SMP Fri Jan 27 02:56:13 UTC 2023
[DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line
mpirun -np 2 gmx_MMPBSA -O -i mmpbsa.in -cs str_noLP.pdb -ci index.ndx -cg 7 3 -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 ]
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.

[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/ai/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/ai/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/ai/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/ai/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/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 7 GMXMMPBSA_REC\n name 3 GMXMMPBSA_LIG\n 7 | 3\n q\n" | /usr/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f str_noLP.pdb
[DEBUG ] :-) GROMACS - gmx make_ndx, 2020.1-Ubuntu-2020.1-1 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
[DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
[DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.1-Ubuntu-2020.1-1
[DEBUG ] Executable: /usr/bin/gmx
[DEBUG ] Data prefix: /usr
[DEBUG ] Working dir: /home/ai/rmcd12-3dfnb(charm36)-gmxMMPDSA分析
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f str_noLP.pdb
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Marie, you're looking more radiant every day!" (Pierre Curie)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 7193 atoms
[DEBUG ] 1 Other : 230 atoms
[DEBUG ] 2 fnb : 47 atoms
[DEBUG ] 3 receptor : 183 atoms
[DEBUG ] 4 Water : 6963 atoms
[DEBUG ] 5 SOL : 6963 atoms
[DEBUG ] 6 non-Water : 230 atoms
[DEBUG ] 7 ligand : 46 atoms
[DEBUG ] 8 receptor_ligand : 229 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 7 'GMXMMPBSA_REC'
[DEBUG ] Copied index group 3 'GMXMMPBSA_LIG'
[DEBUG ] Merged two groups with OR: 46 183 -> 229
[DEBUG ]
[DEBUG ] 9 GMXMMPBSA_REC_GMXMMPBSA_LIG: 229 atoms
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group ligand_receptor (7_3) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /usr/bin/gmx editconf -f str_noLP.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG ] :-) GROMACS - gmx editconf, 2020.1-Ubuntu-2020.1-1 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
[DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
[DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.1-Ubuntu-2020.1-1
[DEBUG ] Executable: /usr/bin/gmx
[DEBUG ] Data prefix: /usr
[DEBUG ] Working dir: /home/ai/rmcd12-3dfnb(charm36)-gmxMMPDSA分析
[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 7193 elements
[DEBUG ] Group 1 ( Other) has 230 elements
[DEBUG ] Group 2 ( fnb) has 47 elements
[DEBUG ] Group 3 ( GMXMMPBSA_LIG) has 183 elements
[DEBUG ] Group 4 ( Water) has 6963 elements
[DEBUG ] Group 5 ( SOL) has 6963 elements
[DEBUG ] Group 6 ( non-Water) has 230 elements
[DEBUG ] Group 7 ( GMXMMPBSA_REC) has 46 elements
[DEBUG ] Group 8 (receptor_ligand) has 229 elements
[DEBUG ] Group 9 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 229 elements
[DEBUG ] Select a group:
[ERROR ] MMPBSA_Error

/usr/bin/gmx editconf failed when querying com_traj.xtc

Check the gmx_MMPBSA.log file to report the problem.

marioernestovaldes · 2023-11-30T00:04:49Z

marioernestovaldes
Nov 30, 2023
Collaborator

This issue typically occurs when the index file is not the correct one... there are plenty of examples in in google group on how to solve this issue

0 replies

afwer1231 · 2024-02-23T03:04:08Z

afwer1231
Feb 23, 2024
Author

Thanks for your reply. Yes, the problem has been solved. I would like to ask how to set the output unit as kJ/mol. With best wishes, Fengwei Ai School of Pharmacy, Xuzhou Medical University E-Mail: ***@***.*** ---- Replied Message ---- | From | Mario E. ***@***.***> | | Date | 11/30/2023 08:05 | | To | ***@***.***> | | Cc | ***@***.***>, ***@***.***> | | Subject | Re: [Valdes-Tresanco-MS/gmx_MMPBSA] gmx editconf failed when querying com_traj.xtc (Discussion #391) | This issue typically occurs when the index file is not the correct one... there are plenty of examples in in google group on how to solve this issue — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

0 replies

marioernestovaldes · 2024-02-23T03:33:14Z

marioernestovaldes
Feb 23, 2024
Collaborator

At the moment the option to transform to Kj/mol is not available...

0 replies

afwer1231 · 2024-02-23T04:43:11Z

afwer1231
Feb 23, 2024
Author

OK. With best wishes, Fengwei Ai School of Pharmacy, Xuzhou Medical University E-Mail: ***@***.*** ---- Replied Message ---- | From | Mario E. ***@***.***> | | Date | 2/23/2024 11:33 | | To | ***@***.***> | | Cc | ***@***.***>, ***@***.***> | | Subject | Re: [Valdes-Tresanco-MS/gmx_MMPBSA] gmx editconf failed when querying com_traj.xtc (Discussion #391) | At the moment the option to transform to Kj/mol is not available... — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

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gmx editconf failed when querying com_traj.xtc #391

afwer1231 Jul 5, 2023

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