[gmx-users] Water mediated hydrogen bonding

Justin Lemkul jalemkul at vt.edu
Thu Jan 15 14:33:31 CET 2015

On 1/15/15 8:31 AM, suhani nagpal wrote:
> Greetings
> I want to calculate hydrogen bonds between solvent molecules and a set of
> residues.
> For that I have created an Index file with:
> 13 (sol) & a OW   (group 1)
> r 1-10 & a H         (group 2)
> But the g_hbond shows error - nothing to be done if I give -num and If I
> give -contact, it does start but fails to read frames.
> Kindly suggest the right approach to evaluate hydrogen bonding between
> solvent molecules and protein residues.

Your index groups are created incorrectly.  If group 2 only has H, the heavy 
atom in the donor is absent, so g_hbond cannot work.  If you want to analyze 
H-bonds between water and residues 1-10, you just need

r 1-10

for make_ndx.  g_hbond figures out which chemical groups participate on its own.

> I also tried reading
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_hbond - it does
> not open.

Works for me.



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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