VMD-L Mailing List

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Fri Sep 16 2005 - 13:01:34 CDT

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