Re: AMBER: heical content in simulations

From: priya priya <>
Date: Tue, 7 Aug 2007 09:41:16 +0100 (BST)

Could you please send me your scripts.

Chng Choon-Peng <> wrote: Dear Priya,

   One possible way is to count the number of residues assigned as part of alpha helices
in your peptide and divide that by the total number of residues.
I wrote a couple of BASH scripts and a C program to process DSSP output
in my study of thermal unfolding, but there might be an easier way?
Doctoral Student (Yr 2.6)
Lab. of Molecular Design (Prof KITAO Akio)
Room 107, Institute of Molecular and Cellular Biosciences
The University of Tokyo
"All my life through, the new sights of Naturemade me rejoice like a child" -- Marie Curie

On 2007/08/07, at 16:58, priya priya wrote:


I want to observe the alpha helix content in my peptide during the simulation(Replica exchange method).
I am using DSSP software to calculate the secondary content but it gives information about ahat type of secondary structure is there and not the helical content.

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Received on Wed Aug 08 2007 - 06:07:34 PDT
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