[AMBER] Contact Map

From: Sourav Purohit <sour000.gmail.com>
Date: Tue, 18 Sep 2018 00:59:06 +0200

Hello all,

I am simulating a protein-DNA complex.
I used the folllowing command to calculate the residue-wise contact map of
the contacts between the protein and the DNA :

trajin 1-combined.trj
nativecontacts :1-60 :61-93 byresidue map mapout 1-contact-map.dat

residue id 1-60 correspond to DNA, while 61-93 correspond to protein.

Is the command line correct or is something needed to be added to this.

The output contact map is a 93 X 93 matrix.
As two masks are specified should we not get a 60 X 33 matrix as the output?
Does this command also calculate the intra-mask contacts?

Thanks in advance for your help and suggestions.
AMBER mailing list
Received on Mon Sep 17 2018 - 14:00:03 PDT
Custom Search