Re: [gmx-users] do_dssp failed to execute
Sunita Patel wrote: *** *Dear Mark, On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote > - Original Message - > From: Sunita Patel > Date: Monday, October 11, 2010 22:50 > Subject: [gmx-users] do_dssp failed to execute > To: Discussion list for GROMACS users > > > Dear User, > > > > I set the path for dssp executable in .bashrc file. Still > > dssp in the path is probably not sufficient. See http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp > I already seen this page and the dssp executable file is present in the specified location. I surprise why it was not working before. I freshly downloaded the dsspcmbi executable and rename it to dssp and gave executable file permission and it started working. I was doing like this earlier also. May be dssp executable was corrupted. I would suspect something else was going on. Note from the error message that the dssp executable was not even invoked: Failed to execute command: /home/sunita/soft/bin -na ... Thus, do_dssp was trying to execute "bin" instead of "dssp." The DSSP environment variable must point to the dssp executable itself, not the PATH to it. Maybe you've got things working now, but do check to make sure you've got your environment properly configured to save yourself headaches later. -Justin Thanks, Sunita > Mark > > > getting following > > error. Could anybody suggest what would be the problem. > > > > error message > > Select a group: 5 > > Selected 5: 'MainChain' > > There are 134 residues in your selected group > > Opening library file > > /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading > > frame0 > > time0.000 > > Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1# > > > > --- > > Program do_dssp, VERSION 4.0.7 > > Source code file: do_dssp.c, line: 471 > > > > Fatal error: > > Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 > > ddZl9dcf > > > /dev/null 2> /dev/null > > ** > > > > Thanks, > > Sunit > > > > > > - > > -- > > gmx-users mailing listgmx-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 Dr. Sunita Patel - Visiting Fellow Department of Chemical Sciences T.I.F.R., Homi Bhabha Road, Colaba Mumbai - 45 - -- 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 listgmx-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
Re: [gmx-users] do_dssp failed to execute
Dear Mark, On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote > - Original Message - > From: Sunita Patel > Date: Monday, October 11, 2010 22:50 > Subject: [gmx-users] do_dssp failed to execute > To: Discussion list for GROMACS users > > > Dear User, > > > > I set the path for dssp executable in .bashrc file. Still > > dssp in the path is probably not sufficient. See > http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp > I already seen this page and the dssp executable file is present in the specified location. I surprise why it was not working before. I freshly downloaded the dsspcmbi executable and rename it to dssp and gave executable file permission and it started working. I was doing like this earlier also. May be dssp executable was corrupted. Thanks, Sunita > Mark > > > getting following > > error. Could anybody suggest what would be the problem. > > > > error message > > Select a group: 5 > > Selected 5: 'MainChain' > > There are 134 residues in your selected group > > Opening library file > > /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading > > frame 0 > > time 0.000 > > Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1# > > > > --- > > Program do_dssp, VERSION 4.0.7 > > Source code file: do_dssp.c, line: 471 > > > > Fatal error: > > Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 > > ddZl9dcf > > > /dev/null 2> /dev/null > > ** > > > > Thanks, > > Sunit > > > > > > - > > -- > > 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 Dr. Sunita Patel - Visiting Fellow Department of Chemical Sciences T.I.F.R., Homi Bhabha Road, Colaba Mumbai - 45 - -- gmx-users mailing listgmx-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
Re: [gmx-users] do_dssp failed to execute
- Original Message - From: Sunita Patel Date: Monday, October 11, 2010 22:50 Subject: [gmx-users] do_dssp failed to execute To: Discussion list for GROMACS users > Dear User, > > I set the path for dssp executable in .bashrc file. Still dssp in the path is probably not sufficient. See http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Mark > getting following > error. Could anybody suggest what would be the problem. > > error message > Select a group: 5 > Selected 5: 'MainChain' > There are 134 residues in your selected group > Opening library file > /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading > frame 0 > time0.000 > Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1# > > --- > Program do_dssp, VERSION 4.0.7 > Source code file: do_dssp.c, line: 471 > > Fatal error: > Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 > ddZl9dcf > > /dev/null 2> /dev/null > ** > > Thanks, > Sunit > > > - > -- > gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] do_dssp failed to execute
Dear User, I set the path for dssp executable in .bashrc file. Still getting following error. Could anybody suggest what would be the problem. error message Select a group: 5 Selected 5: 'MainChain' There are 134 residues in your selected group Opening library file /home/sunita/soft/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1# --- Program do_dssp, VERSION 4.0.7 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 ddZl9dcf > /dev/null 2> /dev/null ** Thanks, Sunit - -- gmx-users mailing listgmx-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
