[gmx-users] naming of CH2 groups in pdb file

Alex Cullen cullena2010 at gmail.com
Thu Sep 10 11:10:28 CEST 2015

Dear Gromacs users,

I have built a pdb file format for a polymer, and I want to use GROMOS FF.
Therefore, I included polar Hydrogens in the pdb file, but I do not know
how to name CH2 groups in NAME and SEGNAME columns. When executing the
pdbtogmx command I receive the following error:
Residue 2 named DEP of a molecule in the input file was mapped to an entry
in the topology database, but the atom CH2 used in an interaction of type
improper in that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.


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