From: John Stone (
Date: Mon Jul 06 2015 - 16:46:03 CDT

  If you have a list of per-residue energies, you should be able to
assign those energy values to something like "beta", or to one of the
per-timestep "user" fields in VMD using a "same residue as" type of
atom selection, and an atom selection "set" command just like the
examples you've seen for other values such as B-factor, etc. Have a look
through some of the VMD tutorials if you haven't already.

  John Stone

On Mon, Jul 06, 2015 at 04:58:54PM +0530, Atreya Dey wrote:
> Hi,
> 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

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