[gmx-users] Problem with Amber99SB-ILDN ff
jalemkul at vt.edu
Mon Jul 8 12:47:15 CEST 2013
On 7/8/13 6:36 AM, Melchor S. wrote:
> I am trying to create the gromacs topology and gro file, using pdb2gmx, with
> the Amber99SB-ILDN ff. The problem is that my protein has two chains, but
> the second one, is a one residue chain, that contains a GLU.
> When I try it I obtain:
> Fatal error:
> In the chosen force field there is no residue type for 'GLU' as a starting
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> Some of you knows how to solve it?
The Amber force fields have different nomenclature than the other force fields.
Terminal residues are prefixed with N and C, so in your case it needs to be
NGLU for the N-terminus.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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