AMBER Archive (2007)

Subject: Re: AMBER: secstruct command

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Thu Jul 19 2007 - 13:22:37 CDT

Dear Anna,

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

Best regards

Holger

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
Germany

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29527
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://mbilab.uni-frankfurt.de
++++++++++++++++++++++++++++++++++++++++++++++++++
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu