[gmx-users] Re: gmx-users Digest, Vol 106, Issue 62

[neeru sharma]

>
> 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
> archive.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> -
>
Thanks Justin.
It worked. Earlier I was trying just with the index file of the specific
residues and without the index file for the specific water molecules. But
now it works when I give the  index file both for specific water and
protein residues.


--Neeru