[gmx-users] Water mediated hydrogen bonding

suhani nagpal suhani.nagpal at gmail.com
Thu Jan 15 14:31:07 CET 2015


I want to calculate hydrogen bonds between solvent molecules and a set of

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.

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

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