Thanks Justin for the reply, how i can sure that it uses the DSSP package correctly , it seems that it just uses the gromacs code : ( Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map ) for some reasons I use gromacs 3.3.3.
On Tue, Jan 1, 2013 at 10:39 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/1/13 2:06 PM, Parisa Rahmani wrote: > >> Hi gmx users >> >> I want to do secondary structure analyze for my trajectory of protein. >> I've downloaded DSSP packages from " >> ftp://ftp.cmbi.ru.nl/pub/**software/dssp/dssp-2.0.4.tgz<ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4.tgz> >> " >> and put it in /usr/local/bin , and rename the folder to dssp. >> when i run "do_dssp -f rmsd.pdb -s protein.tpr -sc scount.xvg -o ss.xpm" >> >> the following appears, >> >> Opening library file /home/parisa/parisa/share/**gromacs/top/phbres.dat >> Opening library file /home/parisa/parisa/share/** >> gromacs/top/aminoacids.dat >> Group 0 ( System) has 420 elements >> Group 1 ( Protein) has 420 elements >> Group 2 ( Protein-H) has 322 elements >> Group 3 ( C-alpha) has 43 elements >> Group 4 ( Backbone) has 128 elements >> Group 5 ( MainChain) has 171 elements >> Group 6 (MainChain+Cb) has 208 elements >> Group 7 ( MainChain+H) has 214 elements >> Group 8 ( SideChain) has 206 elements >> Group 9 ( SideChain-H) has 150 elements >> Select a group: 1 >> Selected 1: 'Protein' >> There are 43 residues in your selected group >> Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map >> Reading frame 0 time 1.000 >> Back Off! I just backed up dd35REJx to ./#dd35REJx.1# >> >> >> and the program is continuously running without .xpm and xvg outputs. >> >> >> i searched the mailing list, but I couldn't find the solution (because >> many of them was about the old DSSP version , that is not available now) >> >> any suggestion would be greatly appreciated. >> >> > do_dssp is very slow. The output files are only produced at the very end, > when the program is done running. For some of my longer trajectories, the > program runs for a few hours. It all depends on how many frames you have > to analyze. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * 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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * 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/Support/Mailing_Lists
