VMD-L Mailing List

From: Tara Sprules (tsprules_at_ualberta.ca)
Date: Wed Oct 16 2002 - 17:34:09 CDT

Hi,

I am new to vmd and am having trouble generating rmsd fits. It seems that
when I first open the program and read in my files and do an rmsd
everything comes back with reasonable values, but if I change my
selections and do another one it falls apart. Most likely I am doing
something wrong, but am having trouble sorting it out.

I am not quite clear on what the correct order is to do things. Basically
I have 10 structures and I would like to write a script that based on the
atom selections I give, will give me the rmsd between each one and the
first molecule eg, as well as moving them so that they are all
superimposed on the first one. (Analogous to doing a superimpose in
Insight). Does anyone have a script that will do that? I'm using vmd-xplor
(vmd version 1.7.1)

Thanks!

Tara

Tara Sprules
Post-Doctoral Fellow
Department of Chemistry
University of Alberta