[gmx-users] Problem with Amber99SB-ILDN ff

[Justin Lemkul]

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
> terminus
> 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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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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