VMD-L Mailing List

From: atila petrosian (atila.petrosian_at_gmail.com)
Date: Mon Jul 12 2010 - 02:19:13 CDT

Hi vmd users

I did simulation of protein-dna interaction by gromacs. I want to obtain
contact map of this protein-dna interaction by vmd.
I want to obtain a contact map such as one of its verticals be protein and
another be dna.I used contact map plug-in
and then VMD Seq Compare window was opened. in this windows, I set
[protein and resid 1 to 70] in Molecule A section and [nucleic and resid
71 to 90] in Molecule B section. then I Selected "fit all", then "Calculate:

Calc res-res Dists". but
no action was occured. there is only a vertical axis of green color which
lists Molecule A resiudes.

please guide me.

any help will highly appreciated