AMBER Archive (2006)

Subject: Re: AMBER: helix content during my simulation

From: Mingfeng Yang (
Date: Mon Feb 06 2006 - 08:03:32 CST

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.


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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