[gmx-users] gmx hbond - specify precise atom names involved
jalemkul at vt.edu
Tue May 3 17:22:47 CEST 2016
On 5/3/16 9:16 AM, Nash, Anthony wrote:
> Hi all,
> Can gmx hbond accept user specified atoms for the donors (default OH and
> NH) and acceptor (default O and N)? I don¹t seem to find any mention of
> this in the -help text.
It's hard-coded in the source, so it's rather inflexible.
> I have a post-trans modified protein from a rather bulk cross-linked
> peptide chain. I defined unique atom times but I have used a unique set of
> atom names.
Create a "fake" topology that uses O,N,H as the first character in applicable
atom names. Then run the analysis using this .tpr file. We did this a while
back with, e.g. thiols and a few others.
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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