[gmx-users] Hbonds analysis

Dario Akaberi dario.aka17 at gmail.com
Sun Dec 11 11:18:20 CET 2016

Hello Khadija,

Do you have a .gro file with both protein "in complex"? if you do you could
try this:

- gmx make_ndx -f proteins_complex.gro -o xxx.ndx

- r x (enter)
- r y  (enter)
- q

where x is the number of the first residue in chain A in the complex.gro
where y is the number of the first residue in chain B in the complex.gro

This should work... At least it worked for me and I just tried with one of
my files.

have a nice day,


On Sun, Dec 11, 2016 at 9:39 AM, 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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