[gmx-users] do_dssp

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 22 22:34:21 CET 2006

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 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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