AMBER Archive (2007)

Subject: Re: AMBER: heical content in simulations

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Fri Nov 09 2007 - 14:25:18 CST

Have you looked at the secstruct (secondary structure) function in ptraj?

On Aug 7, 2007 1:41 AM, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
> 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
> Nature
> made 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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>
>
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