AMBER Archive (2007)

Subject: Re: AMBER: secstruct command

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 19 2007 - 12:46:30 CDT

secstruct uses DSSP, which uses hydrogen bonding, not dihedral angles

On 7/19/07, Anna Díaz Cirac <anna.dcirac_at_gmail.com> wrote:
> Dear Amber users,
>
> how does secstruct command works? I mean... what are the dihedral angles
> that the program use to decide the % of parallel sheet, antiparallel sheet
> .... because i have represented all dihedral values of a 100ns simulation in
> a Ramachandran plot, and using the angles taken from a book about peptides,
> I've calculated the % of the secondary structure and the results are not the
> same. I don't know if Ptraj use a wide range of values that I do.
>
> Another question is...I suppose that the calculation is made to result in
> 100%. If any residue doesn't come to 100%, it's because the program doesn't
> identify it as a structure, does it?
>
> Thanks and regards
>
> --
> Adéu
> Anna
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