Re: [AMBER] H-bond analysis in tetrameric protein complexes

From: Daniel Roe <>
Date: Tue, 16 Jan 2018 09:42:37 -0500


Use the 'nointralmol' keyword to ignore intramolecular hydrogen bonds.


On Mon, Jan 15, 2018 at 4:09 PM, Jag Silwal <> wrote:
> Dear all,
> I have a dimer protein and each of the monomers is binding to another
> protein, giving a total of 4 subunits structure. Usually, when I have a
> simple protein complex I run the following commands and it gives me the
> output with hbavg.out where I can see the fractions, distance, angle and
> all that.
> But when I did the same with this tetrameric complex, looks like I am
> getting hydrogen bonds throughout the complex.
> What I am interested in is the hydrogen bonds between protein a and b in
> the complex of abcd. So I have separated only a.pdb (with prmtop) and
> bcd.pdb (with separate prmtop). a is directly bonded to only b. So I am not
> sure how to insert some kind of mask or something in the script so that I
> only get H-bonds between a and b proteins.
> I run the following commands first :
> parm x.prmtop
> trajin Prod.mdcrd
> hbond HB nointramol out hbond.dat avgout hbavg.dat series uuseries
> solutehb.agr printatomnum dist 3.3 angle 120
> run
> runanalysis lifetime HB[solutehb] out lifehb.dat
> quit
> I would greatly appreciate your help.
> Sincerely,
> Jag Silwal
> Graduate Student, Department of Chemistry
> Michigan State University
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
AMBER mailing list
Received on Tue Jan 16 2018 - 07:00:03 PST
Custom Search