VMD-L Mailing List

From: Jevgenij Raskatov (jraskato_at_ucsc.edu)
Date: Wed May 27 2015 - 20:25:27 CDT

Dear all,

I have a model peptide, for which I would like to calculate alpha helix
content (deviation from an ideal alpha helix) over a trajectory of 50000
steps. I got as far as getting the PLUMED environment set up in VMD, but
everything beyond that was met with little success.

It is a small peptide (10 amino acids) that I am looking at, neutral caps.
Any help would be gratefully appreciated.

Thanks 

-- 
Dr. Jevgenij A. Raskatov
Assistant Professor in Chemistry and Biochemistry
Tel.: +1-831-459-2978
Department of Chemistry and Biochemistry
Physical Science Building 356
1156 High Street
Santa Cruz, CA
95064 USA