[gmx-users] Hbonds analysis

Khadija Amine kh.amine1 at gmail.com
Sun Dec 11 09:40:33 CET 2016

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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