> > 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.
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