Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file
2010/11/10 Justin A. Lemkul <jalem...@vt.edu> > > > ahmet yıldırım wrote: > >> Dear Justin, I don't undertand you said "you haven't chmod +x dssp)?" >> Please look at attached photo? >> >> > I guess that means it's executable; I'm not used to looking into things > with the filesystem browser window. I just couldn't remember if the dssp > executable was, by default, capable of being executed. The command in the > terminal would be what I quoted before. > > Do a test: can you run the dssp executable on a .pdb file? That is, don't > call it via do_dssp, try to use it in its standalone capacity. > > -Justin > > Thanks >> >> >> 2010/11/10 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> >> >> ahmet yıldırım wrote: >> >> Hi, >> >> Please tell me which step is wrong:( >> >> 1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz >> 2.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp >> 3.step-r...@ab-desktop:/home/ab/Desktop/dssp# mv dssp >> /usr/local/bin >> 4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export >> DSSP=/usr/local/bin >> >> >> Your environment variable is wrong. Please read about the proper >> way to set it: >> >> >> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp >> >> Although, if you've got dssp in /usr/local/bin, that's the default >> location where do_dssp expects it, so there is no need to set the >> DSSP environment variable at all. >> >> Perhaps your issue is permission? Or you the dssp executable isn't >> actually executable (i.e., you haven't chmod +x dssp)? >> >> -Justin >> >> 5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr >> -f run.xtc >> >> Program do_dssp, VERSION 4.0.5 >> Source code file: ../../../../src/tools/do_dssp. >> c, line: 471 >> >> *Fatal error:* >> Failed to execute command: /usr/local/bin/dssp -na dduigjCp >> ddDsSuzR > /dev/null 2> /dev/null >> >> >> >> >> 10 Kasım 2010 16:08 tarihinde #ZHAO LINA# <zhao0...@e.ntu.edu.sg >> <mailto:zhao0...@e.ntu.edu.sg> <mailto:zhao0...@e.ntu.edu.sg >> >> <mailto:zhao0...@e.ntu.edu.sg>>> yazdı: >> >> >> http://biskit.pasteur.fr/install/applications/dssp >> >> >> http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html >> >> >> http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp >> >> HTH, >> >> lina >> >> ------------------------------------------------------------------------ >> *From:* gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org> >> <mailto:gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org>> >> >> [gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org> >> <mailto:gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org>>] on behalf of ahmet >> yıldırım >> [ahmedo...@gmail.com <mailto:ahmedo...@gmail.com> >> <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>>] >> >> >> *Sent:* Wednesday, November 10, 2010 10:02 PM >> *To:* Discussion list for GROMACS users >> *Subject:* [gmx-users] DSSP error >> >> Hi, >> >> I installed in /usr/local/bin the DSSP program. And I set the >> environment variable with a command such as "export >> DSSP=/usr/local/bin/dssp". >> a...@ubuntu:/Desktop/work# 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 dduigjCp to ./#dduigjCp.1# >> >> ------------------------------------------------------- >> Program do_dssp, VERSION 4.0.5 >> Source code file: ../../../../src/tools/do_dssp.c, line: 471 >> >> *Fatal error:* >> Failed to execute command: /usr/local/bin/dssp -na dduigjCp >> ddDsSuzR >> > /dev/null 2> /dev/null >> ------------------------------------------------------- >> "Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron >> Bradshaw) >> >> What should I do? >> >> Thanks in advance >> >> -- Ahmet YILDIRIM >> >> -- >> 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
