AMBER Archive (2007)

Subject: Re: AMBER: heical content in simulations

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Tue Aug 07 2007 - 03:41:16 CDT

Could you please send me your scripts.
Regards
priya

Chng Choon-Peng <choonpeng_at_cb.k.u-tokyo.ac.jp> 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?
 
regards,
Choon-Peng
--------------------------------
Doctoral Student (Yr 2.6)
Lab. of Molecular Design (Prof KITAO Akio)
Room 107, Institute of Molecular and Cellular Biosciences
The University of Tokyo
http://www.iam.u-tokyo.ac.jp/MolDes/indexE.html
---------------------------------
"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:

Dear

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.
Regards

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