Hi, I’m new here on the forum, so I’m not sure this is the right place to present my problem.
I am using charmm36-jul2021.ff version and when using pdb2gmx
gmx pdb2gmx -f mypdb.pdb -o processed.gro -ignh
I get the following error:
Start terminus THR-333: NH3+
End terminus GLY-526: COO-
Opening force field file ./charmm36-jul2021.ff/aminoacids.arn
Checking for duplicate atoms....
Now there are 1536 atoms. Deleted 6 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
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Program: gmx pdb2gmx, version 2020.6
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 130)
Fatal error:
Residue 194 named GLY of a molecule in the input file was mapped
to an entry in the topology database, but the atom CB used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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I would like to point out that this only happens with charmm36 and with no other force fields available on gromacs 2020.6. Also if I remove the GLY-526 and leave the CYS-525 as the last residue, everything works.
I suspect that it may be due to having GLY as the last residue of the chain, but I am not expert enough to understand if it is my problem, if it is a bug and, if it is, how to fix it.
Best regards,
Leonardo