GROMACS version:2021.3
GROMACS modification: No
:-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-:
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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
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check out http://www.gromacs.org for more information.
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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 Errors - Gromacs
I didn’t find a solution for this. I would like help.