[gmx-users] pdb2gmx error after switching force fields

Justin Lemkul jalemkul at vt.edu
Fri May 13 16:53:01 CEST 2016

On 5/13/16 10:49 AM, Irem Altan wrote:
> Hi,
> I have a .pdb file that I’ve used in simulations with amber99sb before. I have recently switched to amber03. When I do pdb2gmx, I get the following warning:
> WARNING: WARNING: Residue 26 named GLY of a molecule in the input file was mapped
> to an entry in the topology database, but the atom CB used in
> an interaction of type dihedral in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.

There is an error in the AMBER03 .rtp file.  Either delete the dihedral that 
calls for CB or upgrade your GROMACS version.  I fixed this nearly two years 
ago, so you're using something really outdated :)

> The same thing is repeated for a number of residues (26, 51, 59, 66, 67, 83, 85, 95). The weird thing is, the residue numbers in the pdb file start from 107, and gmx complains about lower numbers. Also, have I understood correctly that gmx complains that glycines in my input file don’t have beta carbons? What could be the problem here?

pdb2gmx uses its own internal numbering, starting from 1.



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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