Hi,
Use the 'nointralmol' keyword to ignore intramolecular hydrogen bonds.
-Dan
On Mon, Jan 15, 2018 at 4:09 PM, Jag Silwal <jagsilwal.gmail.com> 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
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Jan 16 2018 - 07:00:03 PST
