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

Justin Lemkul jalemkul at vt.edu
Thu Sep 10 13:56:56 CEST 2015

On 9/10/15 5:10 AM, Alex Cullen wrote:
> 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.

The atom names in the input coordinate file need to match whatever is specified 
in the .rtp entry.  Since you're dealing with a polymer, surely you've created 
the .rtp entry(ies), so you already know the atom names.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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