Closed Venthaul closed 1 year ago
Valdes-Tresanco-MS
commented
1 year ago This error means that one of the energy terms being computed was extremely large. This is almost always because the PBCs were not removed or an incorrect preparation/selection of the groups. Please make sure your trajectory is consistent (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/gmx_MMPBSA_running/#before-running-gmx_mmpbsa)
derefeq
commented
5 months ago Hello, in my case if it was wrong my trajectory had small jumps (not from one end to the other but it jumped slightly), that was because when removing the pbc using the qwrap tool I first centered everything on the protein and then unwrapped the protein, first is to unwrap the protein and then center. I corrected that thing about the trajectories and I had no problems
Bug summary
Here is my mmpbsa.in file: &general sys_name="Pro-Lig" startframe=1 endframe=5000 / &gb igb=5 saltcon=0.15 / &decomp idecomp=1 print_res="within 6" / After running this input file, the result.dat file cannot be produced and return an error "Some energy terms are undefined." I don't know how to check my trace files, and when I close &decomp, it will not return this error. The original force field I used in simulation is OPLS/AA.
Terminal output
gmx_MMPBSA.log
gmx_MMPBSA.log
```bash [INFO ] Starting gmx_MMPBSA v1.6.1 [DEBUG ] WDIR : /home/wentao/Desktop/GABA_Inhibitor/TM23/MMPBSA_v2 [DEBUG ] AMBERHOME : /home/wentao/miniconda3/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/wentao/miniconda3/envs/gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.10.4 | packaged by conda-forge | (main, Mar 24 2022, 17:38:57) [GCC 10.3.0] [DEBUG ] MPI : /home/wentao/miniconda3/envs/gmxMMPBSA/bin/mpirun [DEBUG ] ParmEd : 3.4.3 [DEBUG ] OS PLATFORM : Linux-5.19.0-40-generic-x86_64-with-glibc2.35 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #41~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 31 16:00:14 UTC 2 [DEBUG ] OS PROCESSOR : x86_64 [INFO ] Command-line mpirun -np 10 gmx_MMPBSA -O -i mmpbsa.in -cs ../MD/md_0_50.tpr -ct ../MD/md_0_50.xtc -ci ../index.ndx -cg 1 13 -cp ../topol.top -o result.dat -eo result.csv [DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |&general [DEBUG ] |sys_name="Pro-Lig" [DEBUG ] |startframe=1 [DEBUG ] |endframe=5000 [DEBUG ] |/ [DEBUG ] |&gb [DEBUG ] |igb=5 [DEBUG ] |saltcon=0.15 [DEBUG ] |/ [DEBUG ] |&decomp [DEBUG ] |idecomp=1 [DEBUG ] |print_res="within 6" [DEBUG ] |/ [DEBUG ] | [DEBUG ] |#mpirun -np 10 gmx_MMPBSA -O -i mmpbsa.in -cs ../MD/md_0_50.tpr -ct ../MD/md_0_50.xtc -ci ../index.ndx -cg 1 13 -cp ../topol.top -o result.dat -eo result.csv [DEBUG ] |-------------------------------------------------------------- [DEBUG ] [INFO ] Checking mmpbsa.in input file... [INFO ] Checking mmpbsa.in input file...Done. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/wentao/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/wentao/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/wentao/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/wentao/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 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n" | /usr/bin/gmx make_ndx -n ../index.ndx -o _GMXMMPBSA_COM_index.ndx -f ../MD/md_0_50.tpr [DEBUG ] :-) GROMACS - gmx make_ndx, 2021.4-Ubuntu-2021.4-2 (-: [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 2021.4-Ubuntu-2021.4-2 [DEBUG ] Executable: /usr/bin/gmx [DEBUG ] Data prefix: /usr [DEBUG ] Working dir: /home/wentao/Desktop/GABA_Inhibitor/TM23/MMPBSA_v2 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n ../index.ndx -o _GMXMMPBSA_COM_index.ndx -f ../MD/md_0_50.tpr [DEBUG ] [DEBUG ] [DEBUG ] Reading structure file [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] [DEBUG ] GROMACS reminds you: "We ignore public understanding of science at our peril." (Eugenie Clark) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] [DEBUG ] 0 System : 223442 atoms [DEBUG ] 1 Protein : 14626 atoms [DEBUG ] 2 Protein-H : 7352 atoms [DEBUG ] 3 C-alpha : 924 atoms [DEBUG ] 4 Backbone : 2772 atoms [DEBUG ] 5 MainChain : 3698 atoms [DEBUG ] 6 MainChain+Cb : 4556 atoms [DEBUG ] 7 MainChain+H : 4576 atoms [DEBUG ] 8 SideChain : 10050 atoms [DEBUG ] 9 SideChain-H : 3654 atoms [DEBUG ] 10 Prot-Masses : 14626 atoms [DEBUG ] 11 non-Protein : 208816 atoms [DEBUG ] 12 Other : 37 atoms [DEBUG ] 13 M23 : 37 atoms [DEBUG ] 14 NA : 211 atoms [DEBUG ] 15 CL : 209 atoms [DEBUG ] 16 Water : 208359 atoms [DEBUG ] 17 SOL : 208359 atoms [DEBUG ] 18 non-Water : 15083 atoms [DEBUG ] 19 Ion : 420 atoms [DEBUG ] 20 M23 : 37 atoms [DEBUG ] 21 NA : 211 atoms [DEBUG ] 22 CL : 209 atoms [DEBUG ] 23 Water_and_ions : 208779 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 13 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 14626 37 -> 14663 [DEBUG ] [DEBUG ] 24 GMXMMPBSA_REC_GMXMMPBSA_LIG: 14663 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group Protein_M23 (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /usr/bin/gmx trjconv -f ../MD/md_0_50.xtc -s ../MD/md_0_50.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.4-Ubuntu-2021.4-2 (-: [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 trjconv, version 2021.4-Ubuntu-2021.4-2 [DEBUG ] Executable: /usr/bin/gmx [DEBUG ] Data prefix: /usr [DEBUG ] Working dir: /home/wentao/Desktop/GABA_Inhibitor/TM23/MMPBSA_v2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../MD/md_0_50.xtc -s ../MD/md_0_50.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Group 0 ( System) has 223442 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 14626 elements [DEBUG ] Group 2 ( Protein-H) has 7352 elements [DEBUG ] Group 3 ( C-alpha) has 924 elements [DEBUG ] Group 4 ( Backbone) has 2772 elements [DEBUG ] Group 5 ( MainChain) has 3698 elements [DEBUG ] Group 6 ( MainChain+Cb) has 4556 elements [DEBUG ] Group 7 ( MainChain+H) has 4576 elements [DEBUG ] Group 8 ( SideChain) has 10050 elements [DEBUG ] Group 9 ( SideChain-H) has 3654 elements [DEBUG ] Group 10 ( Prot-Masses) has 14626 elements [DEBUG ] Group 11 ( non-Protein) has 208816 elements [DEBUG ] Group 12 ( Other) has 37 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 37 elements [DEBUG ] Group 14 ( NA) has 211 elements [DEBUG ] Group 15 ( CL) has 209 elements [DEBUG ] Group 16 ( Water) has 208359 elements [DEBUG ] Group 17 ( SOL) has 208359 elements [DEBUG ] Group 18 ( non-Water) has 15083 elements [DEBUG ] Group 19 ( Ion) has 420 elements [DEBUG ] Group 20 ( M23) has 37 elements [DEBUG ] Group 21 ( NA) has 211 elements [DEBUG ] Group 22 ( CL) has 209 elements [DEBUG ] Group 23 ( Water_and_ions) has 208779 elements [DEBUG ] Group 24 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 14663 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of ../MD/md_0_50.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 10.000 Reading frame 0 time 0.000 [DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "I love fools' experiments. I am always making them." (Charles Darwin) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 24: '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 Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo -e "1"| /usr/bin/gmx trjconv -f ../MD/md_0_50.xtc -s ../MD/md_0_50.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.4-Ubuntu-2021.4-2 (-: [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 trjconv, version 2021.4-Ubuntu-2021.4-2 [DEBUG ] Executable: /usr/bin/gmx [DEBUG ] Data prefix: /usr [DEBUG ] Working dir: /home/wentao/Desktop/GABA_Inhibitor/TM23/MMPBSA_v2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../MD/md_0_50.xtc -s ../MD/md_0_50.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Group 0 ( System) has 223442 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 14626 elements [DEBUG ] Group 2 ( Protein-H) has 7352 elements [DEBUG ] Group 3 ( C-alpha) has 924 elements [DEBUG ] Group 4 ( Backbone) has 2772 elements [DEBUG ] Group 5 ( MainChain) has 3698 elements [DEBUG ] Group 6 ( MainChain+Cb) has 4556 elements [DEBUG ] Group 7 ( MainChain+H) has 4576 elements [DEBUG ] Group 8 ( SideChain) has 10050 elements [DEBUG ] Group 9 ( SideChain-H) has 3654 elements [DEBUG ] Group 10 ( Prot-Masses) has 14626 elements [DEBUG ] Group 11 ( non-Protein) has 208816 elements [DEBUG ] Group 12 ( Other) has 37 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 37 elements [DEBUG ] Group 14 ( NA) has 211 elements [DEBUG ] Group 15 ( CL) has 209 elements [DEBUG ] Group 16 ( Water) has 208359 elements [DEBUG ] Group 17 ( SOL) has 208359 elements [DEBUG ] Group 18 ( non-Water) has 15083 elements [DEBUG ] Group 19 ( Ion) has 420 elements [DEBUG ] Group 20 ( M23) has 37 elements [DEBUG ] Group 21 ( NA) has 211 elements [DEBUG ] Group 22 ( CL) has 209 elements [DEBUG ] Group 23 ( Water_and_ions) has 208779 elements [DEBUG ] Group 24 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 14663 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of ../MD/md_0_50.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 10.000 Reading frame 0 time 0.000 [DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "I love fools' experiments. I am always making them." (Charles Darwin) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 1: '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 M23 (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo -e "13"| /usr/bin/gmx trjconv -f ../MD/md_0_50.xtc -s ../MD/md_0_50.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.4-Ubuntu-2021.4-2 (-: [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 trjconv, version 2021.4-Ubuntu-2021.4-2 [DEBUG ] Executable: /usr/bin/gmx [DEBUG ] Data prefix: /usr [DEBUG ] Working dir: /home/wentao/Desktop/GABA_Inhibitor/TM23/MMPBSA_v2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../MD/md_0_50.xtc -s ../MD/md_0_50.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Group 0 ( System) has 223442 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 14626 elements [DEBUG ] Group 2 ( Protein-H) has 7352 elements [DEBUG ] Group 3 ( C-alpha) has 924 elements [DEBUG ] Group 4 ( Backbone) has 2772 elements [DEBUG ] Group 5 ( MainChain) has 3698 elements [DEBUG ] Group 6 ( MainChain+Cb) has 4556 elements [DEBUG ] Group 7 ( MainChain+H) has 4576 elements [DEBUG ] Group 8 ( SideChain) has 10050 elements [DEBUG ] Group 9 ( SideChain-H) has 3654 elements [DEBUG ] Group 10 ( Prot-Masses) has 14626 elements [DEBUG ] Group 11 ( non-Protein) has 208816 elements [DEBUG ] Group 12 ( Other) has 37 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 37 elements [DEBUG ] Group 14 ( NA) has 211 elements [DEBUG ] Group 15 ( CL) has 209 elements [DEBUG ] Group 16 ( Water) has 208359 elements [DEBUG ] Group 17 ( SOL) has 208359 elements [DEBUG ] Group 18 ( non-Water) has 15083 elements [DEBUG ] Group 19 ( Ion) has 420 elements [DEBUG ] Group 20 ( M23) has 37 elements [DEBUG ] Group 21 ( NA) has 211 elements [DEBUG ] Group 22 ( CL) has 209 elements [DEBUG ] Group 23 ( Water_and_ions) has 208779 elements [DEBUG ] Group 24 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 14663 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of ../MD/md_0_50.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 10.000 Reading frame 0 time 0.000 [DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "I love fools' experiments. I am always making them." (Charles Darwin) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 13: 'GMXMMPBSA_LIG' [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected Amber/OPLS force field topology format... [WARNING] 26557 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1 [INFO ] Assigning PBRadii mbondi2 to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis... [INFO ] Selected 44 residues: R:A:ILE:105 R:A:TYR:348 R:A:PHE:351 R:A:THR:353 R:B:TYR:69 R:B:ILE:72 R:B:SER:73 R:B:GLY:136 R:B:SER:137 R:B:SER:139 R:B:ASN:140 R:B:PHE:189 R:B:HIS:190 R:B:GLY:191 R:B:ARG:192 R:B:THR:200 R:B:SER:202 R:B:LYS:203 R:B:HIS:206 R:B:ILE:263 R:B:VAL:264 R:B:GLU:265 R:B:PRO:266 R:B:ILE:267 R:B:GLN:268 R:B:SER:269 R:B:GLU:270 R:B:GLY:271 R:B:VAL:297 R:B:ASP:298 R:B:GLU:299 R:B:VAL:300 R:B:GLN:301 R:B:THR:302 R:B:GLY:303 R:B:ALA:312 R:B:THR:326 R:B:LYS:329 R:B:PHE:411 R:B:GLY:438 R:B:CYS:439 R:B:ARG:445 R:B:ARG:447 L:C:M23:473 [INFO ] Cleaning normal complex trajectories... [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /usr/bin/gmx trjconv -f ../MD/md_0_50.xtc -s ../MD/md_0_50.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2021.4-Ubuntu-2021.4-2 (-: [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 trjconv, version 2021.4-Ubuntu-2021.4-2 [DEBUG ] Executable: /usr/bin/gmx [DEBUG ] Data prefix: /usr [DEBUG ] Working dir: /home/wentao/Desktop/GABA_Inhibitor/TM23/MMPBSA_v2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../MD/md_0_50.xtc -s ../MD/md_0_50.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] Will write xtc: Compressed trajectory (portable xdr format): xtc [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Reading file ../MD/md_0_50.tpr, VERSION 2022.5 (single precision) [DEBUG ] Group 0 ( System) has 223442 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 14626 elements [DEBUG ] Group 2 ( Protein-H) has 7352 elements [DEBUG ] Group 3 ( C-alpha) has 924 elements [DEBUG ] Group 4 ( Backbone) has 2772 elements [DEBUG ] Group 5 ( MainChain) has 3698 elements [DEBUG ] Group 6 ( MainChain+Cb) has 4556 elements [DEBUG ] Group 7 ( MainChain+H) has 4576 elements [DEBUG ] Group 8 ( SideChain) has 10050 elements [DEBUG ] Group 9 ( SideChain-H) has 3654 elements [DEBUG ] Group 10 ( Prot-Masses) has 14626 elements [DEBUG ] Group 11 ( non-Protein) has 208816 elements [DEBUG ] Group 12 ( Other) has 37 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 37 elements [DEBUG ] Group 14 ( NA) has 211 elements [DEBUG ] Group 15 ( CL) has 209 elements [DEBUG ] Group 16 ( Water) has 208359 elements [DEBUG ] Group 17 ( SOL) has 208359 elements [DEBUG ] Group 18 ( non-Water) has 15083 elements [DEBUG ] Group 19 ( Ion) has 420 elements [DEBUG ] Group 20 ( M23) has 37 elements [DEBUG ] Group 21 ( NA) has 211 elements [DEBUG ] Group 22 ( CL) has 209 elements [DEBUG ] Group 23 ( Water_and_ions) has 208779 elements [DEBUG ] Group 24 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 14663 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of ../MD/md_0_50.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Got Coffee, Got Donuts, Got Wasted" (F. Black) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 24: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] Building AMBER topologies from GROMACS files... Done. [INFO ] Loading and checking parameter files for compatibility... [INFO ] Preparing trajectories for simulation... [INFO ] 5000 frames were processed by cpptraj for use in calculation. [INFO ] Starting calculations in 10 CPUs... [INFO ] Running calculations on normal system... [INFO ] Beginning GB calculations with /home/wentao/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] calculating complex contribution... [INFO ] calculating receptor contribution... [INFO ] calculating ligand contribution... [INFO ] Parsing results to output files... [ERROR ] MMPBSA_Error Some energy terms are undefined. Please, check the input structure and trajectory. Check this section the docs for more info https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/Q%26A/calculations/#possible-solutions Check the gmx_MMPBSA.log file to report the problem. ```Operating system
Ubuntu
gmx_MMPBSA Version
v1.6.1
Python version
3.10.4
Installation
conda AmberTools + pip