[gmx-users] do_dssp

[David van der Spoel]

singh wrote:
> Dear Gromacs users,
> 
> As I am simulating many peptides in a box and do_dssp is only a wrapper for
> calling the program which works on pdb files, I was of the view that it will
> not take PBC into consideration and will probably not assign beta sheets
> very well. Please correct me if I am wrong.
> If this is the case, Is there any other way to assign secondary structure to
> such a system?
> 
many programs do that, e.g. pymol, or VMD, but you have to verify for 
yourself. dssp does not take PBC into account.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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