[gmx-users] Water mediated H-bonds

Justin Lemkul jalemkul at vt.edu
Tue Feb 12 14:10:58 CET 2013

On 2/12/13 1:12 AM, neeru sharma wrote:
> Dear Gromacs Users,
> I have simulated a system of protein-ion complex. As a part of the
> analysis, I want to see whether there are any H-bonds or other interactions
> between the active site residues and the water surrounding those residues.
> I was trying to perform the same using g_hbond program of gromacs, but
> could not get any output. I tried with varying the cut off value and as
> well specifying the "contact" option to look for the non H-bond
> interactions too, that fall within the cut off mentioned.
> Can anybody suggest me how to look for the H-bonds between protein residues
> and water molecules?

Your question and subject line refer to different things.  Detecting hydrogen 
bonds between protein residues and water is trivial.  Create index groups for 
the residues of interest and select these residues and water as the two groups 
for g_hbond.  Water-mediated hydrogen bonds between residues, however, are far 
more difficult to obtain, but this topic has been covered many times in the list 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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