[gmx-users] Water mediated H-bonds

neeru sharma neeru.bioinfo at gmail.com
Tue Feb 12 07:12:54 CET 2013

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?

Any suggestion is welcome!!

Thanks in advance.

Neeru Sharma,
C-DAC, Pune, India

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