From: Hrishikesh Dhondge (hbdhondge_at_gmail.com)
Date: Wed Apr 20 2022 - 01:08:35 CDT
Hello Adrita,
You can get the interprotein contacts using nativecontacts command from
CPPTRAJ. The command will be as follows:
nativecontacts name prot :molA_range :molB_range distance 5.0 noimage
> byresidue writecontacts frame_native_contact.dat
you can specify the same range, for example, your protein is of 10 residues
from 1-10 then as follows:
> nativecontacts name prot :1-10 :1-10 distance 5.0 noimage byresidue
> writecontacts trial_interprot.dat
More information on this can be found here
<https://urldefense.com/v3/__https://amberhub.chpc.utah.edu/nativecontacts/__;!!DZ3fjg!vmEiWxKbD16GFO2xapEwl8hpsA2fsIX94Rh-BCLnO-WKbbql326n1wO7GMEKRp00sQ$ >.
On Tue, Apr 19, 2022 at 4:15 PM Adrita Chakraborty <
chakrabortyadrita652_at_gmail.com> wrote:
> Dear NAMD users'
>
> I want to calculate the inter contacts between two proteins from the psf
> and dcd (trajectory) files.
> Can someone suggest to me how to go about this?
>
>
> Best Regards
> Adrita Chakraborty
>
>
>
-- With regards Hrishikesh Dhondge PhD student, LORIA - INRIA Nancy
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