AMBER Archive (2006)

Subject: Re: AMBER:

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Mon Feb 13 2006 - 15:00:15 CST

Shuli,

I think the newest version of ptraj has a secondary structure analyzer
program in it. You may want to download the newest version and talk to the
author.

Scott

On 2/13/06, shuli kang <kangshuli_at_gmail.com> wrote:
>
> Dear amber users,
> I`m trying to evaluate the secondary structure change of a protein
> during simulations as functions of time. The do_dssp programme in
> GROMACS package could compute the secondary structure for each time
> frame calling the dssp program.
> However, this programme doesn't work with amber trajactory files.
> Maybe some conversion required for this purpose. Could anybody give me
> some suggestion?
>
> Thanks in advance!
>
>
> Shuli.
> --
> Modern Virology Research Center
> College of Life Sciences,
> Wuhan University
> Wuhan, P. R. China, 430072
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