Dear Justin, Finally, The problem is solved, Thank you very much for your patience.
Ps: I set *r...@ab-desktop:/home/ab/Desktop/dssp# export DSSP=/usr/local/bin/dssp* the instead of 4.step but the do_dssp dont run again.The I don't still understand why the DSSP environment variable is not run. Thanks again Final solution: 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz 2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# mv dssp /usr/local/bin 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc Selected 1: 'Protein' There are 164 residues in your selected group Opening library file /usr/share/gromacs/top/ss.map Reading frame 0 time 0.000 Back Off! I just backed up ddqL3oYP to ./#ddqL3oYP.1# Last frame 50 time 10.000 100% gcq#29: "No One Could Foresee the End That Came So Fast" (Slayer) 2010/11/10 Justin A. Lemkul <jalem...@vt.edu> > > > ahmet yıldırım wrote: > >> >> 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz >> 2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC >> 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp >> 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export >> DSSP=/usr/local/bin/dssp >> >> Dear Justin, >> I compiled the program. you said "Your environment variable is wrong", Now >> is it true?? >> >> > Yes, although it's still not necessary. As I said before, if your dssp > binary is in /usr/local/bin/dssp, then that's what Gromacs expects. You > only have to set the DSSP environment variable if you've got the dssp binary > somewhere else. > > -Justin > > Thanks for your helps >> >> 2010/11/10 Ali Naqvi <mna...@ryerson.ca <mailto:mna...@ryerson.ca>> >> >> >> May be the directory you are working in is read only, as Justin >> mentioned this could be a permissions issue. >> As an example the super computer that I use, cannot write anything >> in the home directory, therefore all simulations and analysis are >> done in scratch. >> >> Ali >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Ahmet YILDIRIM >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists