# Error when trying to generate topology with command gmx pdb2gmx -f prot.pdb -o prot\_processed.gro -w **URL:** \ **Category:** User discussions\ **Created:** [October 16, 2021, 8:56pm UTC](https://gromacs.bioexcel.eu/t/error-when-trying-to-generate-topology-with-command-gmx-pdb2gmx-f-prot-pdb-o-prot-processed-gro-w/2968 "2021-10-16T20:56:45Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![brunokdscnwek](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/brunokdscnwek/32/1115_2.png) [@brunokdscnwek](https://gromacs.bioexcel.eu/u/brunokdscnwek)\ **Post date:** [October 16, 2021, 8:56pm UTC](https://gromacs.bioexcel.eu/t/error-when-trying-to-generate-topology-with-command-gmx-pdb2gmx-f-prot-pdb-o-prot-processed-gro-w/2968/1 "2021-10-16T20:56:46Z")
GROMACS version:2021.3 GROMACS modification: No :-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-: ``` GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd ``` 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](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 pdb2gmx, version 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/bruno/Gromacs/5r84test Command line: gmx pdb2gmx -f prot.pdb -o prot\_processed.gro -water spce Select the Force Field: From ‘/usr/share/gromacs/top’: 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9) 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15 Using the Oplsaa force field in directory oplsaa.ff going to rename oplsaa.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b Reading prot.pdb… WARNING: all CONECT records are ignored Read ‘’, 2697 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 1 blocks of water and 628 residues with 2697 atoms chain #res #atoms 1 ‘A’ 304 2373 2 ’ ’ 324 324 (only water) WARNING: there were 11 atoms with zero occupancy and 331 atoms with occupancy unequal to one (out of 2697 atoms). Check your pdb file. Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp Reading residue database… (Oplsaa) Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb * * * Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/utility/futil.cpp (line 442) File input/output error: topol.top ## For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) I didn’t find a solution for this. I would like help.