From: Atreya Dey (
Date: Mon Jul 06 2015 - 06:28:54 CDT


I am new to VMD. I am trying to study binding of two proteins to each
other. I have created a list of residues in both proteins that are within a
certain cut-off from each other using namdenergy. Now, I would like to
color these residues in both proteins based on this calculated energy. If
the energy is highest I want the residue to be in some color (say Blue) and
the lowest energy is colored in a different color (say Red). Can anyone
suggest some method, how I might do this? I have looked at methods that
talk about the use of beta and occupancy values for customized coloring,
but I am not sure how I should manipulate my energy values to use them this
way. Any help will be deeply appreciated.

Atreya Dey,
UG Programme,
IISc - Bangalore