Residue mapped into topology database but atom name not found in file?

[jalemkul]

@amei

Residue 47 named TRP of a molecule in the input file was mapped
to an entry in the topology database, but the atom CH2 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

Either your atom is named incorrectly in the input coordinate file or it’s missing. In the event of the former, rename it to CH2. If the latter, you need to model in any missing atoms using software outside of GROMACS before trying to run pdb2gmx. This is an extremely common error.