[gmx-users] water mediated Hbond

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Mon May 13 14:48:54 CEST 2019

     You can make a ndx file containing the residue of interest and the
SOL. In gmx h-bond command use the index file. It will give you water
mediated hbond

On Tue 7 May, 2019, 12:40 PM , <spss4 at iacs.res.in> wrote:

> Dear all
> I want to determine the water mediated hydrogen between DNA bases and
> small molecule. What extra flag should I use in gmx hbond command? Is
> there any other option to capture the water mediated Hbonds? Please
> suggest something.
> Sunipa Sarkar
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