[AMBER] H-bond analysis in tetrameric protein complexes

From: Jag Silwal <jagsilwal.gmail.com>
Date: Mon, 15 Jan 2018 16:09:44 -0500

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
runanalysis lifetime HB[solutehb] out lifehb.dat

I would greatly appreciate your help.

Jag Silwal
Graduate Student, Department of Chemistry
Michigan State University
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Received on Mon Jan 15 2018 - 13:30:03 PST
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