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?
Regards, Gurpreet Singh On 12/21/06, singh <[EMAIL PROTECTED]> wrote: > > > > > > > > > Dear Gromacs users, > > > > I have simulated 12 peptide fragments in a cubic box and I want to use > do_dssp for secondary structure analysis but I am not sure whether Periodic > boundary conditions will be taken in account during assignment (particularly > for assigning betasheets). > > > > Regards, > > Gurpreet Singh > > ------------------------------------------------- > > University of Dortmund > Department of Chemistry > Physical Chemistry I - Biophysical Chemistry > Otto-Hahn Str. 6 > D-44227 Dortmund > Germany > Office: C1-06 room 176 > Phone: +49 231 755 3916 > > Fax: +49 231 755 3901 > > ------------------------------------------------- But there could be a problem for beta sheets between different chains and for crystal contacts. -- 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 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Hi Gurpreet, The common message is "don't worry, mdrun doesn't write broken molecules". So you're secondary structure will not be affected by periodic boundary conditions. Cheers, Tsjerk _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
