[gmx-users] Calculating hydrogen bonds between specific residues

Justin Lemkul jalemkul at vt.edu
Fri Jan 30 03:19:00 CET 2015

On 1/29/15 9:00 PM, Agnivo Gosai wrote:
> Dear Users
> I want to calculate the number of hydrogen bonds occurring between two
> residues A and B in my biomolecule complex from a production MD run over
> the course of the simulation time.
> I am thinking of the following strategy :-
> 1. Create an index file containing the residue numbers from the .gro file
> of my production run.
> 2. Feed the index file to " g_hbond" , select the two residues of interest
> and run the command.
> My questions are :
> a) While calculating H-bond should I use should I use -nonitacc tag for
> physiological pH ? I am not sure as I do not know the pH value of my
> system. I neutralized the system with Na and Cl ions such that the final
> conc is 0.1 M.

There isn't a pH in your system.  You have a dominant protonation state that you 
have chosen for your molecule(s) of interest that may be those found at some 
given pH, but there is no pH in a classical MD simulation.  Whether or not you 
use -nonitacc depends on what the functional groups are and whether or not you 
should consider N as an acceptor in those cases.

> b) In general is my procedure a correct way of using "g_hbond" ?




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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