VMD-L Mailing List

From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Sun Apr 21 2013 - 13:24:20 CDT

On 4/21/2013 3:10 AM, Ganesh Shahane wrote:
> Dear all,
> Is there a way to calculate the dihedral angles (e.g
> chi1) of a particular amino acid along the entire trajectory using
> VMD? The angle measures should be presented in a graphical format,
> with the measure of angle on Y-axis and time on X-axis.
>
> --
> Ganesh
> MSc Bioinformatics
> University of Pune.

You should look at the "measure dihedral" command
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html

This is a good example:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/13149.html

Someone else has written a TCL script to do this (don't know how well it
works, but it does exist)
https://github.com/ajasja/calculate_dihedrals 

-- 
======================================================================
Jeffrey J. Potoff			  jpotoff_at_wayne.edu
Associate Professor			  Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
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