Error in making protein topology

User discussions
1

I am getting the following error, please help. i am using the command:
gmx pdb2gmx -f pro.pdb -o pro_processed.gro -ter -ff charmm36-jul2022 -ignh
Fatal error:
Residue 12 named GLN 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.

2

Either there is a missing atom in the PDB file or it is incorrectly named. See Common errors when using GROMACS - GROMACS 2024.3 documentation and Residue mapped into topology database but atom name not found in file? - #11 by jalemkul for more information.