[gmx-users] gmx hbond - specify precise atom names involved

Justin Lemkul 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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