AMBER Archive (2007)

Subject: AMBER: secstruct command

From: Anna Díaz Cirac (anna.dcirac_at_gmail.com)
Date: Thu Jul 19 2007 - 12:35:42 CDT

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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