From: Axel Kohlmeyer (
Date: Thu Sep 20 2007 - 09:42:59 CDT

On Wed, 19 Sep 2007, L. Michel Espinoza-Fonseca wrote:

ME> Hi all,
ME> I'm trying to calculate the sidechain-sidechain correlated motions in
ME> a short peptide. I was wondering if there is a script to perform such
ME> task in VMD. Basically I want to determine whether there are concerted
ME> motions between postively charged residues or not.

how about running a principal component analysis on those
residues (sidechains) only?


ME> Thanks!
ME> Michel

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.