AMBER Archive (2006)

Subject: Re: AMBER: helix content during my simulation

From: julien (julien.pecher_at_u-picardie.fr)
Date: Mon Feb 06 2006 - 09:04:51 CST

Thanks,

can send me yours python script? please

thanks for advance

> Usually, I convert snapshots to PDB files from the produced trajectory,
> and then perform dssp analysis on each PDB file.
> This procedure can be automated by a simple python script.
>
> Best,
> Mingfeng
>
> julien wrote:
> > Dear all,
> >
> > I want to "observe" the alpha helix content in my peptide during the
> > simulation.
> > Differents persons use the dssp program. How using the dssp program with
> amber ?
> > is-it with MMTSB or with ptraj or carnal?
> >
> > Sincerely yours
> >
> > best regards
> > julien
> >
> >
>
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-- 
Julien Pecher
Laboratoire de Biophysique, DMAG, INERIS-EA 3901
Faculte de Pharmacie, 1 rue des Louvels
80037 Amiens Cedex 1, France

Tel: +33 (0)3 2282-7786  Fax: +33 (0)3 2282-7469
     +33 (0)3 2282-7498
email: julien.pecher_at_u-picardie.fr
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