Error when trying to generate topology with command gmx pdb2gmx -f prot.pdb -o prot_processed.gro -w

GROMACS version:2021.3
GROMACS modification: No

:-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-:

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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)

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:

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.