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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]: make_prmtops() doesn't like my folder name #164

Closed wrmartin closed 2 years ago

wrmartin commented 2 years ago

Bug summary

I've broken more things! When using the MT approach, I put my topologies in separate folders for complex, receptor and ligand (named as complex, receptor, ligand, with .top files to match). For some reason, make_prmtops() doesn't like this. However, if I rename the complex folder to toppar and point my complex.top file to include toppar/x.itp instead, the complex completes but it fails on the receptor. I've appended then end of such a log file to the bottom of the gmx_MMPBSA.log box.

I'm doing this with the MT approach in the logs, but it fails in the ST approach as well (of course if it fails on the complex there is no difference).

Terminal output

[INFO   ] Starting gmx_MMPBSA v1.5.0+2.gc36d71b
[INFO   ] Command-line
  mpirun -np 16 gmx_MMPBSA MPI -O -i mmpbsa.in -cs complex.pdb -ci complex.ndx -cg 39 36 -ct complex.xtc -cp complex.top -rs ../receptor.pdb -ri ../receptor.ndx -rg 38 -rt ../receptor.xtc -rp receptor.top -ls ../ligand.pdb -li ../ligand.ndx -lg 26 -lt ../ligand.xtc -lp ligand.top -nogui

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /cm/shared/apps/amber/21/bin/cpptraj
[INFO   ] tleap found! Using /cm/shared/apps/amber/21/bin/tleap
[INFO   ] parmchk2 found! Using /cm/shared/apps/amber/21/bin/parmchk2
[INFO   ] sander found! Using /cm/shared/apps/amber/21/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /cm/shared/apps/gromacs/2021.1/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 39_36 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] A receptor structure file was defined. Using MT approach...
[INFO   ] Normal Receptor: Saving group 38 in ../receptor.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] A ligand structure file was defined. Using MT approach...
[INFO   ] Normal Ligand: Saving group 26 in ../ligand.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ]
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
[ERROR  ] MMPBSA_Error Unknown force field in GROMACS topology in line:
 #include "complex/forcefield.itp"
.
           Check the gmx_MMPBSA.log file to report the problem.
  File "/cm/shared/apps/amber/21/miniconda/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/cm/shared/apps/amber/21/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.make_prmtops()
  File "/cm/shared/apps/amber/21/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 535, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/cm/shared/apps/amber/21/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 118, in buildTopology
    tops = self.gmxtop2prmtop()
  File "/cm/shared/apps/amber/21/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 419, in gmxtop2prmtop
    com_top = self.cleantop(self.FILES.complex_top, self.indexes['COM']['COM'])
  File "/cm/shared/apps/amber/21/miniconda/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 673, in cleantop
    GMXMMPBSA_ERROR(f'Unknown force field in GROMACS topology in line:\n {line}')
  File "/cm/shared/apps/amber/21/miniconda/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: Unknown force field in GROMACS topology in line:
 #include "complex/forcefield.itp"

Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 0.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[warn] Epoll MOD(1) on fd 52 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 52 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor

gmx_MMPBSA.log

[INFO ] Starting gmx_MMPBSA v1.5.0+2.gc36d71b [DEBUG ] WDIR : /mnt/beegfs/martinw3/working/Pro/Multi_Test/Single [DEBUG ] AMBERHOME : /cm/shared/apps/amber/21 [DEBUG ] PYTHON EXE : /cm/shared/apps/amber/21/miniconda/bin/python [DEBUG ] PYTHON VERSION: 3.9.5 (default, Jun 4 2021, 12:28:51) [GCC 7.5.0] [DEBUG ] MPI : /usr/mpi/gcc/openmpi-4.0.3rc4/bin/mpirun [DEBUG ] ParmEd : 3.4.1 [DEBUG ] OS PLATFORM : Linux-3.10.0-1062.12.1.el7.x86_64-x86_64-with-glibc2.17 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #1 SMP Tue Feb 4 23:02:59 UTC 2020 [DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line mpirun -np 16 gmx_MMPBSA MPI -O -i mmpbsa.in -cs complex.pdb -ci complex.ndx -cg 39 36 -ct complex.xtc -cp complex.top -rs ../receptor.pdb -ri ../receptor.ndx -rg 38 -rt ../receptor.xtc -rp receptor.top -ls ../ligand.pdb -li ../ligand.ndx -lg 26 -lt ../ligand.xtc -lp ligand.top -nogui

[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 ] |verbose=2,startframe=7501,interval=2 [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 calculation [DEBUG ] |istrng=0.15, fillratio=2.0, radiopt=0, inp=1, [DEBUG ] |/ [DEBUG ] |&decomp [DEBUG ] |idecomp=2, dec_verbose=3, [DEBUG ] |print_res="within 4" [DEBUG ] |-------------------------------------------------------------- [DEBUG ] [INFO ] Checking external programs... [INFO ] cpptraj found! Using /cm/shared/apps/amber/21/bin/cpptraj [INFO ] tleap found! Using /cm/shared/apps/amber/21/bin/tleap [INFO ] parmchk2 found! Using /cm/shared/apps/amber/21/bin/parmchk2 [INFO ] sander found! Using /cm/shared/apps/amber/21/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /cm/shared/apps/gromacs/2021.1/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 39 GMXMMPBSA_REC\n name 36 GMXMMPBSA_LIG\n 39 | 36\n q\n | /cm/shared/apps/gromacs/2021.1/bin/gmx make_ndx -n complex.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx make_ndx, 2021.1 (-: [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 2021.1 [DEBUG ] Executable: /cm/shared/apps/gromacs/2021.1/bin/gmx [DEBUG ] Data prefix: /cm/shared/apps/gromacs/2021.1 [DEBUG ] Working dir: /mnt/beegfs/martinw3/working/Pro/Multi_Test/Single [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n complex.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Always code as if the person who ends up maintaining your code is a violent psychopath who knows where you live." (Martin Golding) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] Counted atom numbers up to 670044 in index file [DEBUG ] [DEBUG ] 0 System : 670044 atoms [DEBUG ] 1 Protein : 36297 atoms [DEBUG ] 2 Protein-H : 18459 atoms [DEBUG ] 3 C-alpha : 2306 atoms [DEBUG ] 4 Backbone : 6918 atoms [DEBUG ] 5 MainChain : 9221 atoms [DEBUG ] 6 MainChain+Cb : 11365 atoms [DEBUG ] 7 MainChain+H : 11412 atoms [DEBUG ] 8 SideChain : 24885 atoms [DEBUG ] 9 SideChain-H : 9238 atoms [DEBUG ] 10 Prot-Masses : 36297 atoms [DEBUG ] 11 non-Protein : 633747 atoms [DEBUG ] 12 Other : 633726 atoms [DEBUG ] 13 TYS : 96 atoms [DEBUG ] 14 CGU : 357 atoms [DEBUG ] 15 BHD : 13 atoms [DEBUG ] 16 CAL : 21 atoms [DEBUG ] 17 ZN2 : 1 atoms [DEBUG ] 18 SOD : 1457 atoms [DEBUG ] 19 POPS : 123444 atoms [DEBUG ] 20 CLA : 464 atoms [DEBUG ] 21 TIP3 : 507894 atoms [DEBUG ] 22 Ion : 21 atoms [DEBUG ] 23 TYS : 96 atoms [DEBUG ] 24 CGU : 357 atoms [DEBUG ] 25 BHD : 13 atoms [DEBUG ] 26 CAL : 21 atoms [DEBUG ] 27 ZN2 : 1 atoms [DEBUG ] 28 SOD : 1457 atoms [DEBUG ] 29 POPS : 123444 atoms [DEBUG ] 30 CLA : 464 atoms [DEBUG ] 31 TIP3 : 507894 atoms [DEBUG ] 32 fVaHC : 11262 atoms [DEBUG ] 33 fVaLC : 10465 atoms [DEBUG ] 34 fXaLC : 2093 atoms [DEBUG ] 35 fXaHC : 3975 atoms [DEBUG ] 36 II : 8968 atoms [DEBUG ] 37 fVa : 21727 atoms [DEBUG ] 38 fXa : 6068 atoms [DEBUG ] 39 Pro : 27795 atoms [DEBUG ] 40 Complex : 36763 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 39 'GMXMMPBSA_REC' [DEBUG ] Copied index group 36 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 27795 8968 -> 36763 [DEBUG ] [DEBUG ] 41 GMXMMPBSA_REC_GMXMMPBSA_LIG: 36763 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group 39_36 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /cm/shared/apps/gromacs/2021.1/bin/gmx editconf -f complex.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb [DEBUG ] :-) GROMACS - gmx editconf, 2021.1 (-: [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 2021.1 [DEBUG ] Executable: /cm/shared/apps/gromacs/2021.1/bin/gmx [DEBUG ] Data prefix: /cm/shared/apps/gromacs/2021.1 [DEBUG ] Working dir: /mnt/beegfs/martinw3/working/Pro/Multi_Test/Single [DEBUG ] Command line: [DEBUG ] gmx editconf -f complex.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb [DEBUG ] [DEBUG ] [DEBUG ] Select a group for output: [DEBUG ] Group 0 ( System) has 670044 elements [DEBUG ] Group 1 ( Protein) has 36297 elements [DEBUG ] Group 2 ( Protein-H) has 18459 elements [DEBUG ] Group 3 ( C-alpha) has 2306 elements [DEBUG ] Group 4 ( Backbone) has 6918 elements [DEBUG ] Group 5 ( MainChain) has 9221 elements [DEBUG ] Group 6 ( MainChain+Cb) has 11365 elements [DEBUG ] Group 7 ( MainChain+H) has 11412 elements [DEBUG ] Group 8 ( SideChain) has 24885 elements [DEBUG ] Group 9 ( SideChain-H) has 9238 elements [DEBUG ] Group 10 ( Prot-Masses) has 36297 elements [DEBUG ] Group 11 ( non-Protein) has 633747 elements [DEBUG ] Group 12 ( Other) has 633726 elements [DEBUG ] Group 13 ( TYS) has 96 elements [DEBUG ] Group 14 ( CGU) has 357 elements [DEBUG ] Group 15 ( BHD) has 13 elements [DEBUG ] Group 16 ( CAL) has 21 elements [DEBUG ] Group 17 ( ZN2) has 1 elements [DEBUG ] Group 18 ( SOD) has 1457 elements [DEBUG ] Group 19 ( POPS) has 123444 elements [DEBUG ] Group 20 ( CLA) has 464 elements [DEBUG ] Group 21 ( TIP3) has 507894 elements [DEBUG ] Group 22 ( Ion) has 21 elements [DEBUG ] Group 23 ( TYS) has 96 elements [DEBUG ] Group 24 ( CGU) has 357 elements [DEBUG ] Group 25 ( BHD) has 13 elements [DEBUG ] Group 26 ( CAL) has 21 elements [DEBUG ] Group 27 ( ZN2) has 1 elements [DEBUG ] Group 28 ( SOD) has 1457 elements [DEBUG ] Group 29 ( POPS) has 123444 elements [DEBUG ] Group 30 ( CLA) has 464 elements [DEBUG ] Group 31 ( TIP3) has 507894 elements [DEBUG ] Group 32 ( fVaHC) has 11262 elements [DEBUG ] Group 33 ( fVaLC) has 10465 elements [DEBUG ] Group 34 ( fXaLC) has 2093 elements [DEBUG ] Group 35 ( fXaHC) has 3975 elements [DEBUG ] Group 36 ( GMXMMPBSA_LIG) has 8968 elements [DEBUG ] Group 37 ( fVa) has 21727 elements [DEBUG ] Group 38 ( fXa) has 6068 elements [DEBUG ] Group 39 ( GMXMMPBSA_REC) has 27795 elements [DEBUG ] Group 40 ( Complex) has 36763 elements [DEBUG ] Group 41 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 36763 elements [DEBUG ] Select a group: [DEBUG ] GROMACS reminds you: "I'd be Safe and Warm if I was in L.A." (The Mamas and the Papas) [DEBUG ] [DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility. [DEBUG ] Read 670044 atoms [DEBUG ] Volume: 6513.5 nm^3, corresponds to roughly 2931000 electrons [DEBUG ] No velocities found [DEBUG ] Selected 41: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] A receptor structure file was defined. Using MT approach... [INFO ] Normal Receptor: Saving group 38 in ../receptor.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo 38 | /cm/shared/apps/gromacs/2021.1/bin/gmx editconf -f ../receptor.pdb -n ../receptor.ndx -o _GMXMMPBSA_REC.pdb [DEBUG ] :-) GROMACS - gmx editconf, 2021.1 (-: [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 2021.1 [DEBUG ] Executable: /cm/shared/apps/gromacs/2021.1/bin/gmx [DEBUG ] Data prefix: /cm/shared/apps/gromacs/2021.1 [DEBUG ] Working dir: /mnt/beegfs/martinw3/working/Pro/Multi_Test/Single [DEBUG ] Command line: [DEBUG ] gmx editconf -f ../receptor.pdb -n ../receptor.ndx -o _GMXMMPBSA_REC.pdb [DEBUG ] [DEBUG ] [DEBUG ] Select a group for output: [DEBUG ] Group 0 ( System) has 672707 elements [DEBUG ] Group 1 ( Protein) has 27499 elements [DEBUG ] Group 2 ( Protein-H) has 13964 elements [DEBUG ] Group 3 ( C-alpha) has 1737 elements [DEBUG ] Group 4 ( Backbone) has 5211 elements [DEBUG ] Group 5 ( MainChain) has 6946 elements [DEBUG ] Group 6 ( MainChain+Cb) has 8568 elements [DEBUG ] Group 7 ( MainChain+H) has 8600 elements [DEBUG ] Group 8 ( SideChain) has 18899 elements [DEBUG ] Group 9 ( SideChain-H) has 7018 elements [DEBUG ] Group 10 ( Prot-Masses) has 27499 elements [DEBUG ] Group 11 ( non-Protein) has 645208 elements [DEBUG ] Group 12 ( Other) has 645195 elements [DEBUG ] Group 13 ( TYS) has 96 elements [DEBUG ] Group 14 ( CGU) has 187 elements [DEBUG ] Group 15 ( BHD) has 13 elements [DEBUG ] Group 16 ( CAL) has 13 elements [DEBUG ] Group 17 ( ZN2) has 1 elements [DEBUG ] Group 18 ( SOD) has 1467 elements [DEBUG ] Group 19 ( POPS) has 124968 elements [DEBUG ] Group 20 ( CLA) has 474 elements [DEBUG ] Group 21 ( TIP3) has 517989 elements [DEBUG ] Group 22 ( Ion) has 13 elements [DEBUG ] Group 23 ( TYS) has 96 elements [DEBUG ] Group 24 ( CGU) has 187 elements [DEBUG ] Group 25 ( BHD) has 13 elements [DEBUG ] Group 26 ( CAL) has 13 elements [DEBUG ] Group 27 ( ZN2) has 1 elements [DEBUG ] Group 28 ( SOD) has 1467 elements [DEBUG ] Group 29 ( POPS) has 124968 elements [DEBUG ] Group 30 ( CLA) has 474 elements [DEBUG ] Group 31 ( TIP3) has 517989 elements [DEBUG ] Group 32 ( fVaHC) has 11262 elements [DEBUG ] Group 33 ( fVaLC) has 10465 elements [DEBUG ] Group 34 ( fXaLC) has 2093 elements [DEBUG ] Group 35 ( fXaHC) has 3975 elements [DEBUG ] Group 36 ( fVa) has 21727 elements [DEBUG ] Group 37 ( fXa) has 6068 elements [DEBUG ] Group 38 ( Complex) has 27795 elements [DEBUG ] Select a group: [DEBUG ] GROMACS reminds you: "Der Ball ist rund, das Spiel dauert 90 minuten, alles andere ist Theorie" (Lola rennt) [DEBUG ] [DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility. [DEBUG ] Read 672707 atoms [DEBUG ] Volume: 6546.22 nm^3, corresponds to roughly 2945700 electrons [DEBUG ] No velocities found [DEBUG ] Selected 38: 'Complex' [INFO ] A ligand structure file was defined. Using MT approach... [INFO ] Normal Ligand: Saving group 26 in ../ligand.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo 26 | /cm/shared/apps/gromacs/2021.1/bin/gmx editconf -f ../ligand.pdb -n ../ligand.ndx -o _GMXMMPBSA_LIG.pdb [DEBUG ] :-) GROMACS - gmx editconf, 2021.1 (-: [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 2021.1 [DEBUG ] Executable: /cm/shared/apps/gromacs/2021.1/bin/gmx [DEBUG ] Data prefix: /cm/shared/apps/gromacs/2021.1 [DEBUG ] Working dir: /mnt/beegfs/martinw3/working/Pro/Multi_Test/Single [DEBUG ] Command line: [DEBUG ] gmx editconf -f ../ligand.pdb -n ../ligand.ndx -o _GMXMMPBSA_LIG.pdb [DEBUG ] [DEBUG ] [DEBUG ] Select a group for output: [DEBUG ] Group 0 ( System) has 479172 elements [DEBUG ] Group 1 ( Protein) has 8798 elements [DEBUG ] Group 2 ( Protein-H) has 4495 elements [DEBUG ] Group 3 ( C-alpha) has 569 elements [DEBUG ] Group 4 ( Backbone) has 1707 elements [DEBUG ] Group 5 ( MainChain) has 2275 elements [DEBUG ] Group 6 ( MainChain+Cb) has 2797 elements [DEBUG ] Group 7 ( MainChain+H) has 2812 elements [DEBUG ] Group 8 ( SideChain) has 5986 elements [DEBUG ] Group 9 ( SideChain-H) has 2220 elements [DEBUG ] Group 10 ( Prot-Masses) has 8798 elements [DEBUG ] Group 11 ( non-Protein) has 470374 elements [DEBUG ] Group 12 ( Other) has 470366 elements [DEBUG ] Group 13 ( CGU) has 170 elements [DEBUG ] Group 14 ( CAL) has 8 elements [DEBUG ] Group 15 ( POPS) has 93218 elements [DEBUG ] Group 16 ( SOD) has 1092 elements [DEBUG ] Group 17 ( CLA) has 346 elements [DEBUG ] Group 18 ( TIP3) has 375540 elements [DEBUG ] Group 19 ( Ion) has 8 elements [DEBUG ] Group 20 ( CGU) has 170 elements [DEBUG ] Group 21 ( CAL) has 8 elements [DEBUG ] Group 22 ( POPS) has 93218 elements [DEBUG ] Group 23 ( SOD) has 1092 elements [DEBUG ] Group 24 ( CLA) has 346 elements [DEBUG ] Group 25 ( TIP3) has 375540 elements [DEBUG ] Group 26 ( II) has 8968 elements [DEBUG ] Select a group: [DEBUG ] GROMACS reminds you: "This isn't right. This isn't even wrong." (Wolfgang Pauli) [DEBUG ] [DEBUG ] Note that major changes are planned in future for editconf, to improve usability and utility. [DEBUG ] Read 479172 atoms [DEBUG ] Volume: 4668.25 nm^3, corresponds to roughly 2100700 electrons [DEBUG ] No velocities found [DEBUG ] Selected 26: 'II' [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [ERROR ] MMPBSA_Error Unknown force field in GROMACS topology in line:

include "complex/forcefield.itp"

. Check the gmx_MMPBSA.log file to report the problem.

Second log snipped:

[INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected CHARMM topology format... [INFO ] Assigning PBRadii mbondi2 to Complex... [INFO ] Writing Normal Complex Amber topology... [INFO ] A Receptor topology file was defined. Using MT approach... [INFO ] Building AMBER Receptor Topology from GROMACS Receptor Topology... [ERROR ] MMPBSA_Error Unknown force field in GROMACS topology in line:

include "rec/forcefield.itp"

. Check the gmx_MMPBSA.log file to report the problem.

Operating system

Linux (Slurm batch system)

gmx_MMPBSA Version

1.5.0

Python version

3.9.5

Installation

No response

marioernestovaldes commented 2 years ago

It seems like there is a problem with the topology files... if this is from charmm-gui, then this:

However, if I rename the complex folder to toppar and point my complex.top file to include toppar/x.itp instead, the complex completes

makes sense as charmm-gui places all the .itp files inside a folder named toppar... Could you please check that the same occurs for the receptor/ligand? if the route to the .itp files in the *.top file is changed or is incorrect, then gmx_MMPBSA can't find those files and throw an error...

wrmartin commented 2 years ago

It seems that it finds the file, but doesn't recognize it. Here are the topology files. The corresponding folders exist (with identical contents), but only topol.top works. Using topol.top with receptor topology files in a folder called receptor (and a receptor.top pointing to them) results in the complex completing its pre-processing and failing when it looks for the receptor files.

It occurred to me that my PRO*.itp files are the same for the complex and the receptor/ligand, so pointing those .top files to a toppar folder works just fine. It's just odd that if my .top file points to a folder not named toppar it fails. Unless there is something hard-coded in the .itp files I don't know about?

topol.txt complex.txt

Valdes-Tresanco-MS commented 2 years ago

Hi Martin. Thanks for helping us to debug gmx_MMPBSA, we appreciated your effort. The problem is very simple. This is a deficiency in the way gmx_MMPBSA cleans up the topology as shown below. https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/blob/fca8ed95e936818d9ebff0cdf19a81375fd3fad7/GMXMMPBSA/make_top.py#L664-L673 The format of CHARMM-GUI or amber is restricted, to prevent users from having unsupported force fields. We are not satisfied with this function, because it is quite simple and primitive, however, its main advantage is that it avoids memory loading of all water molecules and ions. We should improve it soon.

wrmartin commented 2 years ago

Ah ha, that explains why using topparc, topparr, and topparc does work. Thanks for the response!

Valdes-Tresanco-MS commented 2 years ago

Since you mentioned it, I'm taking a look at it and I think I have a better way to clean up the topology, so I'm doing some testing.

Valdes-Tresanco-MS commented 2 years ago

Hi Martin. You can update gmx_MMPBSA from PyPi or conda