Re: AMBER: secstruct command

From: Holger Gohlke <>
Date: Thu, 19 Jul 2007 20:22:37 +0200

Dear Anna,

the implementation of the secstruct command follows the algorithm proposed by
Kabsch & Sander in Biopolymers 1983, 22, 2577-2637.

Best regards


Am Donnerstag, 19. Juli 2007 19:35 schrieb Anna Díaz Cirac:
> 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

Dr. Holger Gohlke
Juniorprofessor fuer Molekulare Bioinformatik
J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut fuer Zellbiologie und Neurowissenschaft
Max-von-Laue-Str. 9
60438 Frankfurt/Main
Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29527
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Received on Sun Jul 22 2007 - 06:07:34 PDT
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