marioernestovaldes
commented
2 years ago Hi there! There was a similar error reported in our google group (https://groups.google.com/g/gmx_mmpbsa/c/fb8YguZCPtA) unfortunately, I didn't receive the files to propose a workaround... Probably one of the values for the periodicity in the prmtop file is zero and this is causing everything to fail... could you please send the files you re using to see if I can come up with a workaround?
thanks in advance...
cheers!
Mario
shiyu-wangbyte
Valdes-Tresanco-MS
Bug summary
run pbsa compute successfully, but an error occur when compute nmode entropy.
Error is "Found an invalid periodicity in the prmtop file: 60"
I have noted that, : pbsa compute via sander, but nmode entropy compute via mmpbsa_py_nabnmode.
is it the reason?
mmpbsa.in is : &general startframe=500, endframe=550, verbose=2, interval=5,use_sander=1, /
&gb igb=5, saltcon=0.150, / &nmode nmstartframe=2, nmendframe=10, nminterval=1, maxcyc=5, drms=2, /
Terminal output
gmx_MMPBSA.log
[INFO ] Starting [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs protein_UNK_prod.tpr -ci protein_UNK_prod.ndx -cg 1 13 -ct protein_UNK_prod.xtc -cp protein_UNK_gmx_solvated.top -nogui
[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead. [WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /soft/amber20/bin/cpptraj [INFO ] tleap found! Using /soft/amber20/bin/tleap [INFO ] parmchk2 found! Using /soft/amber20/bin/parmchk2 [INFO ] sander found! Using /soft/amber20/bin/sander [INFO ] mmpbsa_py_nabnmode found! Using /soft/amber20/bin/mmpbsa_py_nabnmode [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx_mpi found! Using /soft/gromacs/2020v4/bin/gmx_mpi [INFO ] Checking external programs...Done.
[INFO ] Building AMBER Topologies from GROMACS files... [INFO ] Checking gmxMMPBSA data folder exists in Amber data... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [INFO ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [INFO ] No receptor structure file was defined. Using ST approach... [INFO ] Using receptor structure from complex to generate AMBER topology [INFO ] Normal Complex: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [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 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [INFO ] Building Normal Complex Amber Topology... [INFO ] Writing Normal Complex Amber Topology... [INFO ] No Receptor topology files was defined. Using ST approach... [INFO ] Building AMBER Receptor Topology from Complex... [INFO ] No Ligand Topology files was defined. Using ST approach... [INFO ] Building AMBER Ligand Topology from Complex... [INFO ] Cleaning normal complex trajectories... [INFO ] Building AMBER Topologies from GROMACS files...Done. [INFO ] Loading and checking parameter files for compatibility...
Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
GROMACS: gmx make_ndx, version 2020.4 Executable: /soft/gromacs/2020v4/bin/gmx_mpi Data prefix: /soft/gromacs/2020v4 Working dir: /data/shiyu/Thrombin/Thrombin_bcc_ff99SB_restrain_1/1/output Command line: gmx_mpi make_ndx -n protein_UNK_prod.ndx -o _GMXMMPBSA_COM_index.ndx
GROMACS reminds you: "What about my nose?" (Aneesur Rahman, responding to an Argonne manager arguing the long hair of Charles Bennett in his group was disreputing the lab; Retold by Michael Klein)
Going to read 1 old index file(s) Counted atom numbers up to 37518 in index file 0 System : 37518 atoms 1 Protein : 4465 atoms 2 Protein-H : 2240 atoms 3 C-alpha : 276 atoms 4 Backbone : 828 atoms 5 MainChain : 1106 atoms 6 MainChain+Cb : 1360 atoms 7 MainChain+H : 1371 atoms 8 SideChain : 3094 atoms 9 SideChain-H : 1134 atoms 10 Prot-Masses : 4465 atoms 11 non-Protein : 33053 atoms 12 Other : 52 atoms 13 32U : 52 atoms 14 NA : 35 atoms 15 CL : 35 atoms 16 Water : 32931 atoms 17 SOL : 32931 atoms 18 non-Water : 4587 atoms 19 Ion : 70 atoms 20 32U : 52 atoms 21 NA : 35 atoms 22 CL : 35 atoms 23 Water_and_ions : 33001 atoms 24 Protein_32U : 4517 atoms nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index
25 GMXMMPBSA_REC_GMXMMPBSA_LIG: 4517 atoms
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2020.4 Executable: /soft/gromacs/2020v4/bin/gmx_mpi Data prefix: /soft/gromacs/2020v4 Working dir: /data/shiyu/Thrombin/Thrombin_bcc_ff99SB_restrain_1/1/output Command line: gmx_mpi editconf -f protein_UNK_prod.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx
Reading file protein_UNK_prod.tpr, VERSION 2020.4 (single precision) Reading file protein_UNK_prod.tpr, VERSION 2020.4 (single precision)
Select a group for output: Group 0 ( System) has 37518 elements Group 1 ( GMXMMPBSA_REC) has 4465 elements Group 2 ( Protein-H) has 2240 elements Group 3 ( C-alpha) has 276 elements Group 4 ( Backbone) has 828 elements Group 5 ( MainChain) has 1106 elements Group 6 ( MainChain+Cb) has 1360 elements Group 7 ( MainChain+H) has 1371 elements Group 8 ( SideChain) has 3094 elements Group 9 ( SideChain-H) has 1134 elements Group 10 ( Prot-Masses) has 4465 elements Group 11 ( non-Protein) has 33053 elements Group 12 ( Other) has 52 elements Group 13 ( GMXMMPBSA_LIG) has 52 elements Group 14 ( NA) has 35 elements Group 15 ( CL) has 35 elements Group 16 ( Water) has 32931 elements Group 17 ( SOL) has 32931 elements Group 18 ( non-Water) has 4587 elements Group 19 ( Ion) has 70 elements Group 20 ( 32U) has 52 elements Group 21 ( NA) has 35 elements Group 22 ( CL) has 35 elements Group 23 ( Water_and_ions) has 33001 elements Group 24 ( Protein_32U) has 4517 elements Group 25 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4517 elements Select a group: GROMACS reminds you: "I'm An Oakman" (Pulp Fiction)
Note that major changes are planned in future for editconf, to improve usability and utility. Read 37518 atoms Volume: 376.536 nm^3, corresponds to roughly 169400 electrons Velocities found Selected 25: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' :-) GROMACS - gmx editconf, 2020.4 (-: :-) GROMACS - gmx editconf, 2020.4 (-:
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2020.4 Executable: /soft/gromacs/2020v4/bin/gmx_mpi Data prefix: /soft/gromacs/2020v4 Working dir: /data/shiyu/Thrombin/Thrombin_bcc_ff99SB_restrain_1/1/output Command line: gmx_mpi editconf -f protein_UNK_prod.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx Reading file protein_UNK_prod.tpr, VERSION 2020.4 (single precision) Reading file protein_UNK_prod.tpr, VERSION 2020.4 (single precision)
Select a group for output: Group 0 ( System) has 37518 elements Group 1 ( GMXMMPBSA_REC) has 4465 elements Group 2 ( Protein-H) has 2240 elements Group 3 ( C-alpha) has 276 elements Group 4 ( Backbone) has 828 elements Group 5 ( MainChain) has 1106 elements Group 6 ( MainChain+Cb) has 1360 elements Group 7 ( MainChain+H) has 1371 elements Group 8 ( SideChain) has 3094 elements Group 9 ( SideChain-H) has 1134 elements Group 10 ( Prot-Masses) has 4465 elements Group 11 ( non-Protein) has 33053 elements Group 12 ( Other) has 52 elements Group 13 ( GMXMMPBSA_LIG) has 52 elements Group 14 ( NA) has 35 elements Group 15 ( CL) has 35 elements Group 16 ( Water) has 32931 elements Group 17 ( SOL) has 32931 elements Group 18 ( non-Water) has 4587 elements Group 19 ( Ion) has 70 elements Group 20 ( 32U) has 52 elements Group 21 ( NA) has 35 elements Group 22 ( CL) has 35 elements Group 23 ( Water_and_ions) has 33001 elements Group 24 ( Protein_32U) has 4517 elements Group 25 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4517 elements Select a group: GROMACS reminds you: "Louis Pasteur's theory of germs is ridiculous fiction." (Pierre Pachet, Professor of Physiology at Toulouse, 1872) Note that major changes are planned in future for editconf, to improve usability and utility. Read 37518 atoms Volume: 376.536 nm^3, corresponds to roughly 169400 electrons Velocities found Selected 1: 'GMXMMPBSA_REC' :-) GROMACS - gmx editconf, 2020.4 (-:
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
GROMACS: gmx editconf, version 2020.4 Reading file protein_UNK_prod.tpr, VERSION 2020.4 (single precision) Reading file protein_UNK_prod.tpr, VERSION 2020.4 (single precision)
Select a group for output: Group 0 ( System) has 37518 elements Group 1 ( GMXMMPBSA_REC) has 4465 elements Group 2 ( Protein-H) has 2240 elements Group 3 ( C-alpha) has 276 elements Group 4 ( Backbone) has 828 elements Group 5 ( MainChain) has 1106 elements Group 6 ( MainChain+Cb) has 1360 elements Group 7 ( MainChain+H) has 1371 elements Group 8 ( SideChain) has 3094 elements Group 9 ( SideChain-H) has 1134 elements Group 10 ( Prot-Masses) has 4465 elements Group 11 ( non-Protein) has 33053 elements Group 12 ( Other) has 52 elements Group 13 ( GMXMMPBSA_LIG) has 52 elements Group 14 ( NA) has 35 elements Group 15 ( CL) has 35 elements Group 16 ( Water) has 32931 elements Group 17 ( SOL) has 32931 elements Group 18 ( non-Water) has 4587 elements Group 19 ( Ion) has 70 elements Group 20 ( 32U) has 52 elements Group 21 ( NA) has 35 elements Group 22 ( CL) has 35 elements Group 23 ( Water_and_ions) has 33001 elements Group 24 ( Protein_32U) has 4517 elements Group 25 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4517 elements Select a group: GROMACS reminds you: "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)
Note that major changes are planned in future for editconf, to improve usability and utility. Note that major changes are planned in future for editconf, to improve usability and utility. Read 37518 atoms Volume: 376.536 nm^3, corresponds to roughly 169400 electrons Velocities found Selected 13: 'GMXMMPBSA_LIG' :-) GROMACS - gmx trjconv, 2020.4 (-:
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx trjconv, version 2020.4 Executable: /soft/gromacs/2020v4/bin/gmx_mpi Data prefix: /soft/gromacs/2020v4 Working dir: /data/shiyu/Thrombin/Thrombin_bcc_ff99SB_restrain_1/1/output Command line: gmx_mpi trjconv -f protein_UNK_prod.xtc -s protein_UNK_prod.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
Will write xtc: Compressed trajectory (portable xdr format): xtc Reading file protein_UNK_prod.tpr, VERSION 2020.4 (single precision) Reading file protein_UNK_prod.tpr, VERSION 2020.4 (single precision) Group 0 ( System) has 37518 elements Group 1 ( GMXMMPBSA_REC) has 4465 elements Group 2 ( Protein-H) has 2240 elements Group 3 ( C-alpha) has 276 elements Group 4 ( Backbone) has 828 elements Group 5 ( MainChain) has 1106 elements Group 6 ( MainChain+Cb) has 1360 elements Group 7 ( MainChain+H) has 1371 elements Group 8 ( SideChain) has 3094 elements Group 9 ( SideChain-H) has 1134 elements Group 10 ( Prot-Masses) has 4465 elements Group 11 ( non-Protein) has 33053 elements Group 12 ( Other) has 52 elements Group 13 ( GMXMMPBSA_LIG) has 52 elements Group 14 ( NA) has 35 elements Group 15 ( CL) has 35 elements Group 16 ( Water) has 32931 elements Group 17 ( SOL) has 32931 elements Group 18 ( non-Water) has 4587 elements Group 19 ( Ion) has 70 elements Group 20 ( 32U) has 52 elements Group 21 ( NA) has 35 elements Group 22 ( CL) has 35 elements Group 23 ( Water_and_ions) has 33001 elements Group 24 ( Protein_32U) has 4517 elements Group 25 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4517 elements GROMACS reminds you: "Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron Bradshaw) Back Off! I just backed up COM_traj_0.xtc to ./#COM_traj_0.xtc.1# -> frame 0 time 0.000 ^M^MReading frame 1 time 5.000 -> frame 1 time 5.000 ^M^MReading frame 2 time 10.000 -> frame 2 time 10.000 ^M^MReading frame 3 time 15.000 -> frame 3 time 15.000 ^M^MReading frame 4 time 20.000 -> frame 4 time 20.000 ^M^MReading frame 5 time 25.000 -> frame 5 time 25.000 ^M^MReading frame 6 time 30.000 -> frame 6 time 30.000 ^M^MReading frame 7 time 35.000 -> frame 7 time 35.000 ^M^MReading frame 8 time 40.000 -> frame 8 time 40.000 ^M^MReading frame 9 time 45.000 -> frame 9 time 45.000 ^M^MReading frame 10 time 50.000 -> frame 10 time 50.000 ^M^MReading frame 11 time 55.000 ^MReading frame 12 time 60.000 ^MReading frame 13 time 65.000 ^MReading frame 14 time 70.000 ^MReading frame 15 time 75.000 ^MReading frame 16 time 80.000 ^MReading frame 17 time 85.000 ^MReading frame 18 time 90.000 ^MReading frame 19 time 95.000 ^MReading frame 20 time 100.000 -> frame 20 time 100.000 ^M^MReading frame 30 time 150.000 -> frame 30 time 150.000 ^M^MReading frame 40 time 200.000 -> frame 40 time 200.000 ^M^MReading frame 50 time 250.000 -> frame 50 time 250.000 ^M^MReading frame 60 time 300.000 -> frame 60 time 300.000 ^M^MReading frame 70 time 350.000 -> frame 70 time 350.000 ^M^MReading frame 80 time 400.000 -> frame 80 time 400.000 ^M^MReading frame 90 time 450.000 -> frame 90 time 450.000 ^M^MReading frame 100 time 500.000 -> frame 100 time 500.000 ^M^MReading frame 110 time 550.000 -> frame 110 time 550.000 ^M^MReading frame 120 time 600.000 -> frame 120 time 600.000 ^M^MReading frame 130 time 650.000 -> frame 130 time 650.000 ^M^MReading frame 140 time 700.000 -> frame 140 time 700.000 ^M^MReading frame 150 time 750.000 -> frame 150 time 750.000 ^M^MReading frame 160 time 800.000 -> frame 160 time 800.000 ^M^MReading frame 170 time 850.000 -> frame 170 time 850.000 ^M^MReading frame 180 time 900.000 -> frame 180 time 900.000 ^M^MReading frame 190 time 950.000 -> frame 190 time 950.000 ^M^MReading frame 200 time 1000.000 -> frame 200 time 1000.000 ^M -> frame 210 time 1050.000 ^M -> frame 220 time 1100.000 ^M -> frame 230 time 1150.000 ^M -> frame 240 time 1200.000 ^M -> frame 250 time 1250.000 ^M -> frame 260 time 1300.000 ^M -> frame 270 time 1350.000 ^M -> frame 280 time 1400.000 ^M -> frame 290 time 1450.000 ^M^MReading frame 300 time 1500.000 -> frame 300 time 1500.000 ^M -> frame 310 time 1550.000 ^M -> frame 320 time 1600.000 ^M -> frame 330 time 1650.000 ^M -> frame 340 time 1700.000 ^M -> frame 350 time 1750.000 ^M -> frame 360 time 1800.000 ^M -> frame 370 time 1850.000 ^M -> frame 380 time 1900.000 ^M -> frame 390 time 1950.000 ^M^MReading frame 400 time 2000.000 -> frame 400 time 2000.000 ^M -> frame 410 time 2050.000 ^M -> frame 420 time 2100.000 ^M -> frame 430 time 2150.000 ^M -> frame 440 time 2200.000 ^M -> frame 450 time 2250.000 ^M -> frame 460 time 2300.000 ^M -> frame 470 time 2350.000 ^M -> frame 480 time 2400.000 ^M -> frame 490 time 2450.000 ^M^MReading frame 500 time 2500.000 -> frame 500 time 2500.000 ^M -> frame 510 time 2550.000 ^M -> frame 520 time 2600.000 ^M -> frame 530 time 2650.000 ^M -> frame 540 time 2700.000 ^M -> frame 550 time 2750.000 ^M -> frame 560 time 2800.000 ^M -> frame 570 time 2850.000 ^M -> frame 580 time 2900.000 ^M -> frame 590 time 2950.000 ^M^MReading frame 600 time 3000.000 -> frame 600 time 3000.000 ^M -> frame 610 time 305 Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 25: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
Operating system
opensuse(linux)
gmx_MMPBSA Version
gmx_MMPBSA v1.4.3 based on MMPBSA version 16.0 and AmberTools 20
Python version
Python 3.7.7
Installation
conda AmberTools + conda