[gmx-users] hbond analysis

Justin Lemkul jalemkul at vt.edu
Thu Oct 30 13:17:17 CET 2014

On 10/30/14 7:58 AM, Urszula Uciechowska wrote:
> Dear gromacs users,
> I am having some problems with hbond analysis using gromacs. I am
> interested in hbonds between certain amino acids for example: LYS256 and
> nucleic acid that has number 2 in my files. I generated the index file
> which contains r256 and r2 by running make_ndx -f gro -o out.ndx
> then I run g_hbond
> g_hbond -f traj.xtc -s .tpr -num hydrogen-bonds-protein.xvg

Well, that can't be your command because it doesn't use the index file.  Always 
copy and paste; please don't try to recreate what you did.

> My xvg file did not contain any hbond between those amino acids, which is
> not true. I do not know what went wrong. Could anyone suggest me
> something?

Have you verified that the index groups contain what you think they do?  What 
does gmxcheck tell you?

> Is there any other way to run the hbond?

No, there is one program for analyzing hydrogen bonds and it's g_hbond.

> Is it possible to use the xtc trajectory and run hbond anlysis in ptraj?
> or can I convert it somehow?

It's always possible to convert formats.  The question is whether or not you 
want or need to spend the time doing it.  If g_hbond does not detect any 
hydrogen bonds, either (1) there are none that fit the criteria or (2) your 
index groups don't correspond to what you think they do.



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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