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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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