Gromacs fatal error version 2021

User discussions
1

GROMACS version:2021
GROMACS modification: Yes/No
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 151)

Fatal error:
Residue 137 named SER of a molecule in the input file was mapped
to an entry in the topology database, but the atom OG 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 Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

The program has a list of atoms it expects for any given residue and it seems residue 137 in your input file is missing an atom. You may need to open the input file to see whether something’s been mislabeled, and if there really are atoms missing then finding a new input file with all the atoms may be the most straightforward solution

3

If i understand, I need to use a software able to the missing atoms in my protein.
Thank you for your explanation, I’ll try it