[gmx-users] Hbonds analysis

Amir Zeb zebamir85 at gmail.com
Sun Dec 11 11:08:24 CET 2016

go to gro file and find out the atom number from which your concerned
residue starats and ends
copy the atom numbers inbetween and make a separate selection in your index
file for residues and paste therein
you will have the residue number once you prompt by putting hbond
good luck

On Dec 11, 2016 5:40 PM, "Khadija Amine" <kh.amine1 at gmail.com> wrote:

> Dear Gromacs users,
> I'm simulating a system of protein-protein complex.
> One of the interesting analysis I would like to perform is to compute H
> bonds between two important residues.
>  I want to  plot a graph of one specific residue located in the first
> protein (chain A) that make hydrogen bond interactions with another
> interface residue in the second protein (chain B). I just want to analyze
> how many times residue 1 make or lose the interactions with residue 2
> during the whole simulation (time frame : 20ns) .​
> If someone can help me make index for the residue 1 in the chain A and
> residue 2 in the chain B.
> Thank you
> *Khadija AMINE*
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
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