I do not have any problem. The problem is solved. Thank you very much
10 Kasım 2010 22:45 tarihinde Justin A. Lemkul <jalem...@vt.edu> yazdı: > > > ahmet yıldırım wrote: > >> 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. >> >> > I'm confused. You say the problem is solved, then you say that do_dssp is > not running, but then your output below indicates that everything is fine. > > If there is still a problem, please list all your commands in exact order > (not "this instead of that"). > > To eliminate any sort of confusion, please stop setting the DSSP > environment variable if your dssp binary is in /usr/local/bin. As I keep > telling you, if this is its location, it is exactly what Gromacs expects and > you do not need it whatsoever. You only need to set DSSP if your binary is > in some other location. > > -Justin > > 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 <mailto: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> <mailto: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> >> <mailto: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> >> <mailto: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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- 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