Re: [gmx-users] DSSP installation on Ubuntu 12.10
On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] DSSP installation on Ubuntu 12.10
Hi Justin, Sorry for the mistake, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? On Saturday, October 12, 2013 12:55 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] DSSP installation on Ubuntu 12.10
On 10/11/13 8:12 AM, Mass wrote: Hi Justin, Sorry for the mistake, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? Check for typos. If the file is actually there, has the right permissions (readable), and has that name, it is impossible to trigger the fatal error. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] DSSP installation on Ubuntu 12.10
Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? Thanks On Saturday, October 12, 2013 1:12 AM, Mass masstransfer_2...@yahoo.com wrote: Hi Justin, Sorry for the mistake, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? On Saturday, October 12, 2013 12:55 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] DSSP installation on Ubuntu 12.10
On 10/11/13 8:57 AM, Mass wrote: Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? It depends on your shell. In bash, you can just add the line that sources GMXRC to .bashrc. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] DSSP installation on Ubuntu 12.10
Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue. Google knows a lot more about it than anybody here ;-) Mark On Fri, Oct 11, 2013 at 2:57 PM, Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? Thanks On Saturday, October 12, 2013 1:12 AM, Mass masstransfer_2...@yahoo.com wrote: Hi Justin, Sorry for the mistake, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? On Saturday, October 12, 2013 12:55 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] DSSP installation on Ubuntu 12.10
Dear Gromacs users, I have asked this questions before and Justin gave some answers which I could solve my problem based on his answer. I am using Ubuntu 12.10 and installed gromacs 4.5.5-2. this is what I have done 2- I moved this file to usr/local/bin 1- first I downloaded the dssp wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O~/dssp 2- I moved this file to usr/local/bin then I run do_dssp and I was asked to select a group Select a group: 1 Selected 1: 'Protein' There are 162 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 Back Off! I just backed up ddQ0FCUF to ./#ddQ0FCUF.1# after that I am getting Program do_dssp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddQ0FCUF ddzUlAvc /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I really appreciate if anyone can tell me simple and step-by step solution (I am a beginner user). Thanks -- 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] DSSP installation on Ubuntu 12.10
Hi, Since the release of 4.5.5, DSSP totally changed its command-line interface. So old GROMACS code cannot work with new DSSP. You need to get the old version of DSSP to use with old GROMACS, or new GROMACS code to work with either DSSP. Mark On Thu, Oct 10, 2013 at 1:37 PM, Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs users, I have asked this questions before and Justin gave some answers which I could solve my problem based on his answer. I am using Ubuntu 12.10 and installed gromacs 4.5.5-2. this is what I have done 2- I moved this file to usr/local/bin 1- first I downloaded the dssp wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64-O~/dssp 2- I moved this file to usr/local/bin then I run do_dssp and I was asked to select a group Select a group: 1 Selected 1: 'Protein' There are 162 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Back Off! I just backed up ddQ0FCUF to ./#ddQ0FCUF.1# after that I am getting Program do_dssp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddQ0FCUF ddzUlAvc /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I really appreciate if anyone can tell me simple and step-by step solution (I am a beginner user). Thanks -- 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
Re: [gmx-users] DSSP installation on Ubuntu 12.10
Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors any comments? Thanks -- 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
