[gmx-users] Missing terminal cap group

[Justin Lemkul]

On 7/3/15 11:10 AM, anu chandra wrote:
> Dear Gromacs users,
>
> I am trying to generate topology for a membrane protein, which is capped
> with acetyl and methyl amide group, using Charmm36 force field in Gromacs.
> Unfortunately, the acetyl (ACE) group is seems to be missing in the Gromacs
> Charmm36 force field. Can anybody suggest me a way to add acetyl group with
> Charmm36 force field?
>

The ACE capping group is present in the force field .rtp, so it's not missing. 
If it's not in your coordinate file, then you need to build it with some 
external software.  The GROMACS website has some suggestions for that.

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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