[gmx-users] GLY dihedrals in amber03 family force fields

Justin Lemkul jalemkul at vt.edu
Wed Oct 29 13:38:19 CET 2014

On 10/29/14 8:35 AM, Tomek Wlodarski wrote:
> Hi,
> I looked into amber03w topology file for amino acids and I found that GLY
> has interesting dihedral defined:
>      -C     N    CA    CB
> Which gives me warnings with pdb2gmx:
> WARNING: WARNING: Residue 75 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.
> I looked into amber03 main paper but I have not found anything related...
> Any idea why this dihedral is defined for GLY?

Glycine doesn't have a beta carbon.  Whoever created that file made a mistake.



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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