VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Fri Sep 16 2005 - 16:24:51 CDT

Hi!

if by advanced plugin you mean the RMSDTT, first, thanks for the
complement, and second, it should be able to calculate the rmsd of a
trajectory agains an average of the same trajectory (look for the 'Ave'
radiobutton). I would, thought, check it agains a couple of simple
structures first, I must said, I did try to check things when
programming the plugin, but the 'ave' option was not tested that much,
since I don't use frequently.

Best,

Luis

Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021

Tel: (212) 746-6375
Fax: (212) 746-8690
lug2002_at_med.cornell.edu

Kara Di Giorgio said the following on 09/16/05 14:01:
> I need to calculate RMSDs for a series of trajectories compared to a
> "base" structure. I have trajectories for the "base" structure and all
> of my other molecules. I've played around with the RMSD function in VMD
> (and downloaded the advanced plugin), but I need to generate an average
> structure of the last 50 steps of my "base" trajectory and save it as a
> pdb to use it as the reference. Has anyone created a script to do
> this? I generated my trajectories in Amber.
>
> Thank you for any help,
>
> Kara Di Giorgio
> University of the Pacific
> Stockton, CA
>