[gmx-users] DSSP output
Hi ALL, Is there any way to get the percentage of each secondary structural content of a protein using do_dssp if I supply a single PDB to it? And how to plot the data of the -sc output from do_dssp? Any suggestion is welcome. Regards, Anirban -- 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 output
On 11/7/13 8:24 AM, Anirban wrote: Hi ALL, Is there any way to get the percentage of each secondary structural content of a protein using do_dssp if I supply a single PDB to it? The output of scount.xvg has the percentages, but it's also trivial to do it for one snapshot. The contents of scount.xvg are the number of residues present in each type of secondary structure, and you know the total number of residues... And how to plot the data of the -sc output from do_dssp? Like any multiple data set. xmgrace -nxy -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 problem
On 10/13/13 11:56 PM, Mass wrote: Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l -rw--- 1 Mass Mass 15351454992 Aug 21 07:51 bLac_orig_md2.trr Try giving readable permissions to all, i.e. chmod +r. With I/O errors, the answer is always one of: (1) file does not exist, (2) file has wrong permissions, or (3) cannot write to disk for space or permission reasons. -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 problem
Hi Justin Here is the copied and pasted output Mass@Mass-ThinkPad-Edge-E530:~/bLac_run_simulations_200ns_analyzed/original$ ls -l total 92332632 -rw-rw-r-- 1 Mass Mass 0 Sep 8 19:46 310Helix.dat -rw--- 1 Mass Mass 371878 Aug 21 07:39 3BLG_115XrayWater.top -rw-rw-r-- 1 Mass Mass 282249 Sep 8 19:46 aHelix.dat -rw-rw-r-- 1 Mass Mass 12963 Sep 9 20:00 average.pdb -rw-rw-r-- 1 Mass Mass 12962 Aug 22 21:49 #average.pdb.1# -rw-rw-r-- 1 Mass Mass 12963 Sep 1 20:18 #average.pdb.2# -rw-rw-r-- 1 Mass Mass 39371 Aug 23 10:50 bLac_orig_md2-3_atomic-sas.xvg -rw-rw-r-- 1 Mass Mass 1180585 Aug 22 22:20 bLac_orig_md2-3_radius-of-gyration.xvg -rw-rw-r-- 1 Mass Mass6151 Aug 23 10:50 bLac_orig_md2-3_residue-sas.xvg -rw-rw-r-- 1 Mass Mass 538412 Aug 22 20:15 bLac_orig_md2-3_rmsd-Calpha-vs-start.xvg -rw-rw-r-- 1 Mass Mass2791 Aug 22 21:49 bLac_orig_md2-3_rmsf-per-residue.xvg -rw-rw-r-- 1 Mass Mass 6739262 Aug 23 13:33 bLac_orig_md2-3_SecStruc.dat -rw-rw-r-- 1 Mass Mass 1180736 Aug 23 10:50 bLac_orig_md2-3_solvent-accessible-surface.xvg -rw-rw-r-- 1 Mass Mass 815104 Aug 23 10:32 #bLac_orig_md2-3_solvent-accessible-surface.xvg.1# -rw-rw-r-- 1 Mass Mass 4696839648 Aug 22 15:58 bLac_orig_md2-3.xtc -rw--- 1 Mass Mass 1539720 Aug 21 06:31 bLac_orig_md2.cpt -rw--- 1 Mass Mass 7561608 Aug 21 06:31 bLac_orig_md2.edr -rw--- 1 Mass Mass 4412810 Aug 21 06:31 bLac_orig_md2.gro -rw--- 1 Mass Mass 7213156 Aug 21 07:39 bLac_orig_md2.log -rw--- 1 Mass Mass 1539720 Aug 21 06:31 bLac_orig_md2_prev.cpt -rw--- 1 Mass Mass 2075808 Aug 21 07:39 bLac_orig_md2.tpr -rw--- 1 Mass Mass 15351454992 Aug 21 07:51 bLac_orig_md2.trr -rw--- 1 Mass Mass 2348494832 Aug 21 06:41 bLac_orig_md2.xtc -rw-rw-r-- 1 Mass Mass 7045242668 Sep 1 18:41 bLac_orig_md3-4.xtc -rw--- 1 Mass Mass 1539720 Aug 21 06:19 bLac_orig_md3.cpt -rw--- 1 Mass Mass 7561608 Aug 21 06:19 bLac_orig_md3.edr -rw--- 1 Mass Mass 4412810 Aug 21 06:19 bLac_orig_md3.gro -rw--- 1 Mass Mass 7212876 Aug 21 06:31 bLac_orig_md3.log -rw--- 1 Mass Mass 1539720 Aug 21 06:19 bLac_orig_md3_prev.cpt -rw--- 1 Mass Mass 2075808 Aug 21 06:31 bLac_orig_md3.tpr -rw--- 1 Mass Mass 15351454992 Aug 21 07:39 bLac_orig_md3.trr -rw--- 1 Mass Mass 2348579612 Aug 21 06:31 bLac_orig_md3.xtc -rw-rw-r-- 1 Mass Mass 39519 Sep 9 20:54 bLac_orig_md4-5_atomic-sas.xvg -rw-rw-r-- 1 Mass Mass 39542 Sep 1 21:56 #bLac_orig_md4-5_atomic-sas.xvg.1# -rw-rw-r-- 1 Mass Mass 2360604 Sep 9 20:11 bLac_orig_md4-5_radius-of-gyration.xvg -rw-rw-r-- 1 Mass Mass 2360602 Sep 1 21:02 #bLac_orig_md4-5_radius-of-gyration.xvg.1# -rw-rw-r-- 1 Mass Mass6135 Sep 9 20:54 bLac_orig_md4-5_residue-sas.xvg -rw-rw-r-- 1 Mass Mass6158 Sep 1 21:56 #bLac_orig_md4-5_residue-sas.xvg.1# -rw-rw-r-- 1 Mass Mass 1098421 Sep 9 19:50 bLac_orig_md4-5_rmsd-Calpha-vs-start.xvg -rw-rw-r-- 1 Mass Mass 1098406 Sep 1 19:37 #bLac_orig_md4-5_rmsd-Calpha-vs-start.xvg.1# -rw-rw-r-- 1 Mass Mass2815 Sep 9 20:00 bLac_orig_md4-5_rmsf-per-residue.xvg -rw-rw-r-- 1 Mass Mass2799 Sep 1 20:18 #bLac_orig_md4-5_rmsf-per-residue.xvg.1# -rw-rw-r-- 1 Mass Mass 6739262 Sep 8 19:45 bLac_orig_md4-5_SecStruct.dat -rw-rw-r-- 1 Mass Mass 2360697 Sep 9 20:54 bLac_orig_md4-5_solvent-accessible-surface.xvg -rw-rw-r-- 1 Mass Mass 2360696 Sep 1 21:56 #bLac_orig_md4-5_solvent-accessible-surface.xvg.1# -rw-rw-r-- 1 Mass Mass 9393557496 Sep 1 18:53 bLac_orig_md4-5.xtc -rw--- 1 Mass Mass 1539720 Aug 21 06:19 bLac_orig_md4.cpt -rw--- 1 Mass Mass 7561608 Aug 21 06:08 bLac_orig_md4.edr -rw--- 1 Mass Mass 4412810 Aug 21 06:08 bLac_orig_md4.gro -rw--- 1 Mass Mass 7212890 Aug 21 06:08 bLac_orig_md4.log -rw--- 1 Mass Mass 1539720 Aug 21 04:58 bLac_orig_md4_prev.cpt -rw--- 1 Mass Mass 2075808 Aug 21 06:08 bLac_orig_md4.tpr -rw--- 1 Mass Mass 15351454992 Aug 21 06:19 bLac_orig_md4.trr -rw--- 1 Mass Mass 2348637800 Aug 21 05:08 bLac_orig_md4.xtc -rw--- 1 Mass Mass 1539720 Aug 21 04:58 bLac_orig_md5.cpt -rw--- 1 Mass Mass 7561608 Aug 21 04:58 bLac_orig_md5.edr -rw--- 1 Mass Mass 4412810 Aug 21 04:58 bLac_orig_md5.gro -rw--- 1 Mass Mass 7212675 Aug 21 04:58 bLac_orig_md5.log -rw--- 1 Mass Mass 1539720 Aug 21 06:08 bLac_orig_md5_prev.cpt -rw--- 1 Mass Mass 2075808 Aug 21 04:58 bLac_orig_md5.tpr -rw--- 1 Mass Mass 15351454992 Aug 21 06:08 bLac_orig_md5.trr -rw--- 1 Mass Mass 2348549636 Aug 21 06:19 bLac_orig_md5.xtc -rw--- 1 Mass Mass 10315 Aug 21 07:39 bLac_orig.p1n14-c.69215.err -rw--- 1 Mass Mass 0 Aug 21 07:39 bLac_orig.p1n14-c.69215.out -rw--- 1 Mass Mass 10312 Aug 21 06:31
[gmx-users] DSSP problem
Dear users; I am trying to run DSSP and have problem, 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? -- 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 problem
On 10/12/13 6:08 PM, Mass wrote: Dear users; I am trying to run DSSP and have problem, 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? Please provide the copied and pasted output of ls -l in that directory. -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 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
[gmx-users] dssp works fine, but do_dssp gives fatal error
Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 works fine, but do_dssp gives fatal error
Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 works fine, but do_dssp gives fatal error
Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 works fine, but do_dssp gives fatal error
Right. And what is its location? On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 works fine, but do_dssp gives fatal error
The location of dssp is /usr/local/bin/dssp On Wed, Jun 12, 2013 at 3:43 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Right. And what is its location? On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 works fine, but do_dssp gives fatal error
Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 works fine, but do_dssp gives fatal error
Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 works fine, but do_dssp gives fatal error
You have (at least) two easy options. 1) Install old_dssp that is available through the dssp web page. 2) Install a newer version of gromacs than you have at the moment. What version do you currently use? Erik On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 works fine, but do_dssp gives fatal error
My current Gromacs version is 4.5.5 I think using the first option will be easy and quick. On Wed, Jun 12, 2013 at 4:41 PM, Erik Marklund er...@xray.bmc.uu.se wrote: You have (at least) two easy options. 1) Install old_dssp that is available through the dssp web page. 2) Install a newer version of gromacs than you have at the moment. What version do you currently use? Erik On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 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 core dumped
Hi Rama, I bet that wasn't the only output you got. Two things can usually happen with do_dssp. Either you chose the wrong group for analysis, or there is a problem with the version of DSSP. Probably the latter: DSSP syntax changed recently, and I think that GMX 4.5.5 can't deal with that. There should be capital punishment on syntax changes on such programs... Try digging up an older version of DSSP. Cheers, Tsjerk On Thu, Oct 4, 2012 at 11:18 AM, rama david ramadavidgr...@gmail.com wrote: hi Gromacs Friend i Install dssp 2.0.4 . I am using gromacs 4.5.5 I put dssp in /usr/local/bin I try with export DSSP=/usr/local/bin/dssp When Run dssp with simple pdb file it run but when I run do_dssp command i got following output.. Segmentation fault (core dumped) (dssp -h DSSP 2.0.4 options: -h [ --help ] Display help message ) I also goes through archive but not find out the answer. Please tel me how to figure out these problem With best wishes and regards.. rama david -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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 doubt
Hi all, I downloaded the original form of DSSP which is recently called DSSPold. Whenever I use the following: *do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm * It selects Protein by it-self without any control from me. I want to choose from the list, for example not protein but C-alpha. To solve this probIem, I prepared the index file which includes only C-alphas of my system. Then, I use the following: *do_dssp -s topol.tpr -f traj.xtc -n C_alpha.ndx* I get the below fatal error: Program do_dssp, VERSION 4.5.4 Source code file: do_dssp.c, line: 566 Fatal error: Failed to execute command: /home_palamut2/mguler/dssp/dsspcmbi -na ddcblxTU ddq8aNVV /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Are there any suggestions or corrections? Thanks in advance.. Turgay -- 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 doubt
On 6/7/12 10:07 AM, Turgay Cakmak wrote: Hi all, I downloaded the original form of DSSP which is recently called DSSPold. Whenever I use the following: *do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm * It selects Protein by it-self without any control from me. I want to choose from the list, for example not protein but C-alpha. That shouldn't happen. You should be prompted for a selection. Note that selecting only C-alpha atoms will not work. DSSP requires all MainChain atoms to be considered, since the secondary structure criteria are based on hydrogen bonding distances. An incorrect selection could explain the error you get below. -Justin To solve this probIem, I prepared the index file which includes only C-alphas of my system. Then, I use the following: *do_dssp -s topol.tpr -f traj.xtc -n C_alpha.ndx* I get the below fatal error: Program do_dssp, VERSION 4.5.4 Source code file: do_dssp.c, line: 566 Fatal error: Failed to execute command: /home_palamut2/mguler/dssp/dsspcmbi -na ddcblxTU ddq8aNVV /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Are there any suggestions or corrections? Thanks in advance.. Turgay -- Justin A. Lemkul, Ph.D. Research Scientist 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] dssp doubt
Hi Justin, Thank you for your descriptive reply. I prepared new index.file which includes mainchain, and when I used the do_dssp with -n index.ndx, it worked. But, if I doesn't use the index file, again, the Protein is selected by the system. It is weird.. Best regards, Deniz On Thu, Jun 7, 2012 at 5:10 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 6/7/12 10:07 AM, Turgay Cakmak wrote: Hi all, I downloaded the original form of DSSP which is recently called DSSPold. Whenever I use the following: *do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm * It selects Protein by it-self without any control from me. I want to choose from the list, for example not protein but C-alpha. That shouldn't happen. You should be prompted for a selection. Note that selecting only C-alpha atoms will not work. DSSP requires all MainChain atoms to be considered, since the secondary structure criteria are based on hydrogen bonding distances. An incorrect selection could explain the error you get below. -Justin To solve this probIem, I prepared the index file which includes only C-alphas of my system. Then, I use the following: *do_dssp -s topol.tpr -f traj.xtc -n C_alpha.ndx* I get the below fatal error: Program do_dssp, VERSION 4.5.4 Source code file: do_dssp.c, line: 566 Fatal error: Failed to execute command: /home_palamut2/mguler/dssp/**dsspcmbi -na ddcblxTU ddq8aNVV /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/**Documentation/Errorshttp://www.gromacs.org/Documentation/Errors Are there any suggestions or corrections? Thanks in advance.. Turgay -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 configuration in Gromacs 4.5.5
Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. Thanks in advance. -- -- Regards, N. Sathishkumar, -- 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 configuration in Gromacs 4.5.5
On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- 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 configuration in Gromacs 4.5.5
Dear Sir, Thank u for reply and the old dssp executable was working fine, [root@localhost]# dssp COPYRIGHT W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 CMBI version by elmar.krie...@cmbi.ru.nl / April 1, 2010 USAGE dssp [Options] PDB_File DSSP_File - Read PDB_File and write DSSP_File dssp [Options] -- dssp_file - Read from stdin and write DSSP_File dssp -h - Display this help screen OPTIONS -na Disables the calculation of accessible surface. -cClassic (old) format. -wWide 2002 format (for future use,not the current standard). -vVerbose. --Read from standard input. -h -? Prints a help message. -VPrints version, as in first line of the output. ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS By emmanuel.cource...@toulouse.inra.fr -ssa Adds information about disulfide bonds to output file -xRenames residues with incomplete sidechains to 'X' -alt2 Keeps an additional AltLoc indicator at the line ends [root@localhost]# and i have checked one again the path of DSSP [root@localhost sathish]# echo $DSSP /usr/local/bin/dssp [root@localhost sathish]# but while running with do_dssp has problem. [root@localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx -o ss.xpm :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5-dev-20120318-375fa98 (-: . . . Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Segmentation fault (core dumped) [root@localhost sathish]# Am not clear to understand this problem. help me -- -- Regards, N. Sathishkumar, sath...@khu.ac.kr On Wed, May 16, 2012 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 configuration in Gromacs 4.5.5
On 16/05/2012 5:33 PM, Sathish wrote: Dear Sir, Thank u for reply and the old dssp executable was working fine, [root@localhost]# dssp COPYRIGHT W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 CMBI version by elmar.krie...@cmbi.ru.nl mailto:elmar.krie...@cmbi.ru.nl / April 1, 2010 USAGE dssp [Options] PDB_File DSSP_File - Read PDB_File and write DSSP_File dssp [Options] -- dssp_file - Read from stdin and write DSSP_File dssp -h - Display this help screen OPTIONS -na Disables the calculation of accessible surface. -cClassic (old) format. -wWide 2002 format (for future use,not the current standard). -vVerbose. --Read from standard input. -h -? Prints a help message. -VPrints version, as in first line of the output. ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS By emmanuel.cource...@toulouse.inra.fr mailto:emmanuel.cource...@toulouse.inra.fr -ssa Adds information about disulfide bonds to output file -xRenames residues with incomplete sidechains to 'X' -alt2 Keeps an additional AltLoc indicator at the line ends [root@localhost]# and i have checked one again the path of DSSP [root@localhost sathish]# echo $DSSP /usr/local/bin/dssp [root@localhost sathish]# but while running with do_dssp has problem. [root@localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx -o ss.xpm :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5-dev-20120318-375fa98 (-: You are not using 4.5.5. If you'd shown this the first time, you'd have used less of everybody's time. Maybe this version is one that is updated to use the new DSSP. Maybe you should go and use 4.5.5. Also, don't do routine work logged in as root, unless you like reinstalling your whole operating system. Mark . . . Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Segmentation fault (core dumped) [root@localhost sathish]# Am not clear to understand this problem. help me -- -- Regards, N. Sathishkumar, mailto:sath...@khu.ac.kr On Wed, May 16, 2012 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- 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 -- 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 download,installation and dssp plot
Hello friends, I am facing problem in using DSSP. I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP Plot ,It generate .dssp file,which have values .But i want the DSSP PLot.Please tell me the installation procedure and download link to get the dssp plot. Thanks bunty -- 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 download,installation and dssp plot
On 14/05/2012 4:14 PM, bunty xy wrote: Hello friends, I am facing problem in using DSSP. I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP Plot ,It generate .dssp file,which have values .But i want the DSSP PLot.Please tell me the installation procedure and download link to get the dssp plot. This forum is for GROMACS-related questions. It is not apparent to me that the plot you seek is GROMACS-related. Perhaps another forum, or the DSSP documentation is what you need. Mark -- 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-last GROMACS 4.5.7 can not use DSSP -please help to solve it
Dear ALL:how to install DSSP in Gromacs4.5.7I followed someone replies mail still can not use do I do right ?DSSP website-miscellaneous-distribution-dsspold-linux distribution then get dsspcmbibut Gromacs can not recoginz this index gromacs index is do_dssp ?and DSSPagain , how to install DSSP in Gromacs ?many thanks Best Wishesli-hua -- 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-last GROMACS 4.5.7 can not use DSSP -please help to solve it
You set the environment variable DSSP to the absolute path to your dssp executable. Then do_sddp can make use of it. Is that clear? Erik 26 apr 2012 kl. 09.33 skrev 李 麗花: Dear ALL: how to install DSSP in Gromacs4.5.7 I followed someone replies mail still can not use do I do right ? DSSP website-miscellaneous-distribution-dsspold-linux distribution then get dsspcmbi but Gromacs can not recoginz this index gromacs index is do_dssp ? and DSSP again , how to install DSSP in Gromacs ? many thanks Best Wishes li-hua -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 error
hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 400 time 400.000 Back Off! I just backed up ddbXn2WY to ./#ddbXn2WY.1# --- Program do_dssp, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It's just the way this stuff is done (Built to Spill) -- 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 error
What's your dssp version? The most recent ones have different flags that are not yet supported by gromacs. Erik 27 mar 2012 kl. 11.50 skrev Albert: hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 400 time 400.000 Back Off! I just backed up ddbXn2WY to ./#ddbXn2WY.1# --- Program do_dssp, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It's just the way this stuff is done (Built to Spill) -- 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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 error
Hi, I used to have similar problem. Try using double precision. Worked for me. Best Quoting Albert mailmd2...@gmail.com: hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 400 time 400.000 Back Off! I just backed up ddbXn2WY to ./#ddbXn2WY.1# --- Program do_dssp, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- It's just the way this stuff is done (Built to Spill) Rohit Arora Laboratoire de Biologie et de Pharmacologie Génétique Appliquée (CNRS UMR 8113) Ecole Normale Supérieure, Cachan France Bureau: +33 (0) 1 47 40 77 49 Portable: +33 (0) 6 23 85 12 46 -- 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 error
On 27/03/2012 8:50 PM, Albert wrote: hello: I am trying to run do_dssp by command: do_dssp -s md.tpr -f md.trr -b 400 -e 500 -o fws_ss.xpm but it said: Select a group: 1 Selected 1: 'Protein' There are 35 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 400 time 400.000 Back Off! I just backed up ddbXn2WY to ./#ddbXn2WY.1# --- Program do_dssp, VERSION 4.5.5 Source code file: do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddbXn2WY ddeWknkk /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Sounds like you haven't followed the instructions in do_dssp -h carefully enough. Mark -- 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 and gromacs version
On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Ha ... the dssp complain the segmentation fault in 4.5.5, but can run smoothly in 4.5.3. IIRC, seems there were some threads talked about that before. Mark -- 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 -- 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 and gromacs version
Gromacs' 4.5.5 do_dssp is broken. There is a patch for it in git. I haven't tried it out, so I can't say for sure it works. This is not a DSSP problem, it's a Gromacs problem. Just to reinforce the idea, the new DSSP should not be used, no matter which Gromacs version you're using. Best regards, Joao Henriques On Fri, Mar 2, 2012 at 9:10 AM, lina lina.lastn...@gmail.com wrote: On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Ha ... the dssp complain the segmentation fault in 4.5.5, but can run smoothly in 4.5.3. IIRC, seems there were some threads talked about that before. Mark -- 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 -- João Henriques -- 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 and gromacs version
Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, -- 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 and gromacs version
On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Mark -- 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 problem
On 25/12/2010 11:03 PM, mustafa bilsel wrote: Hi Justin, maybe I am making a mistake with installation. What I am doing is this: I am creating a diretory called DSSP, then I write rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ http://rsync.cmbi.ru.nl/dssp/ /home/m/DSSP/ on the terminal, and then file transfer starts. Then I write export DSSP=/home/m/DSSP/dssp (pointing the exe file). In above procedures there is NO INSTALLATION. If any installation is required? We don't support DSSP. Please read their instructions and follow them. If you can't follow them, please communicate the problem to them so they can fix it. Another important thing is that I couldn't copy dssp to anywhere with copy dssp /. command, but I can do it cp -r dssp / It means that dssp isnot a file, it seems a folder. And I also see uncompressed zip explanation near the dssp. OK, so if it's a folder, open it and look for the executable to work out its fully-qualified name... I have written axactly what I did so far. No, you've used some frustrating ellipses, instead of copying and pasting from your terminal, thereby leaving us the option of presuming you've done something wrong. Mark Maybe it will help you to understand the mistake. Thank you for your kind interests best wishes Mustafa -- 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 problem
http://biskit.pasteur.fr/install/applications/dssp wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip unzip dsspcmbi.zip cd dssp ./DsspCompileGCC cd .. sudo mv dssp /usr/local/src/ cd /usr/local/bin sudo ln -s ../src/dssp/dsspcmbi . lina On Sat, Dec 25, 2010 at 8:45 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 25/12/2010 11:03 PM, mustafa bilsel wrote: Hi Justin, maybe I am making a mistake with installation. What I am doing is this: I am creating a diretory called DSSP, then I write rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /home/m/DSSP/ on the terminal, and then file transfer starts. Then I write export DSSP=/home/m/DSSP/dssp (pointing the exe file). In above procedures there is NO INSTALLATION. If any installation is required? We don't support DSSP. Please read their instructions and follow them. If you can't follow them, please communicate the problem to them so they can fix it. Another important thing is that I couldn't copy dssp to anywhere with copy dssp /. command, but I can do it cp -r dssp / It means that dssp isnot a file, it seems a folder. And I also see uncompressed zip explanation near the dssp. OK, so if it's a folder, open it and look for the executable to work out its fully-qualified name... I have written axactly what I did so far. No, you've used some frustrating ellipses, instead of copying and pasting from your terminal, thereby leaving us the option of presuming you've done something wrong. Mark Maybe it will help you to understand the mistake. Thank you for your kind interests best wishes Mustafa -- 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
mustafa bilsel wrote: Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. The proper setting for the environment variable is explained in great detail here: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note the line If this is not the case, you must set the DSSP environment variable accordingly, pointing to the actual dssp executable, not just the PATH to it. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Learn what your shell uses and apply it. You're more than likely running bash, in which case export is the command to use. -Justin -- 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
[gmx-users] dssp problem
Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Best wishes -- 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 problem
On Fri, Dec 24, 2010 at 11:38 AM, mustafa bilsel mfbil...@gmail.com wrote: Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. You should issue: export DSSP=/home/m/DSSP See, /home/m/DSSP is actually the /path/to/dssp in your case. Terry And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? Best wishes -- 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
Hi, I have a problem with dssp programme. I have the programme in /home/m/DSSP. When I write export DSSP=/usr/local/bin and then I check /usr/local/bin I couldn't see dssp. How can I handle this problem. I have caheceked gromacs website export DSSP=/path/to/dssp setenv DSSP /path/to/dssp commands are written. Could you write export DSSP=/path/to/dssp command according to me. And also I use Ubuntu 10.04, setenv is not used, if I try to install it, I see the package not found message. What should I do about it? -- 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 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 time0.000 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 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 error
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 [gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [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 time0.000 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 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 error
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 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 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 [gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [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 time0.000 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 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 -- Ahmet YILDIRIM -- 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 error
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 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 [gmx-users-boun...@gromacs.org mailto:gmx-users-boun...@gromacs.org] on behalf of ahmet yıldırım [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 time0.000 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 listgmx-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 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 error
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 time0.000 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 listgmx-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
Re: [gmx-users] DSSP error
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 time0.000 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 listgmx-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
Re: [gmx-users] DSSP error
Justin A. Lemkul wrote: ahmet yıldırım wrote: Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file That seems to indicate that the dssp executable does not match your architecture. Get rid of this executable and compile it from source, which I believe is provided when you download dssp. ...or check whether or not dssp is actually executable, as I suggested twice before. -Justin -Justin 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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
Re: [gmx-users] DSSP error
ahmet yıldırım wrote: Dear Justin, Thanks for your replies a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb bash: /usr/local/bin/dssp: cannot execute binary file That seems to indicate that the dssp executable does not match your architecture. Get rid of this executable and compile it from source, which I believe is provided when you download dssp. -Justin 2010/11/10 Justin A. Lemkul jalem...@vt.edu mailto: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 mailto: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 mailto: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 mailto: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 mailto: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 mailto: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
Re: [gmx-users] DSSP error
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 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 error
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?? Thanks for your helps 2010/11/10 Ali Naqvi 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 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 -- Ahmet YILDIRIM -- 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 error
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 listgmx-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 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 error
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 time0.000 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 listgmx-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 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 -- Ahmet YILDIRIM -- 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 error
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 time0.000 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 listgmx-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 listgmx-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] DSSP error
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 time0.000 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 listgmx-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 listgmx-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
[gmx-users] dssp
Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Thanks for any advice, lina -- 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
#ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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] dssp
Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 -- 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
What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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-us...@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 list gmx-us...@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
Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 -- 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 -- 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] dssp
I did choose 1 protein when it asked me to choose. Thanks for your answering, I may try on my desktop another time. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Linus Östberg [bio...@talavis.eu] Sent: Friday, November 05, 2010 9:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 -- 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 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
Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 -- 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 -- 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 -- 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
But right now I noticed something a bit funny, Try different times, Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# --- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax /dev/null 2 /dev/null Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k /dev/null 2 /dev/null was something wrong with mine DSSP, except path reason. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Friday, November 05, 2010 9:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] dssp Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul
Re: [gmx-users] dssp
#ZHAO LINA# wrote: But right now I noticed something a bit funny, Try different times, Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# --- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax /dev/null 2 /dev/null Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k /dev/null 2 /dev/null was something wrong with mine DSSP, except path reason. I still think you're setting your DSSP environment variable wrong. Please consult the link I posted before - you have to point DSSP to the *actual executable* not the directory that contains it, i.e.: WRONG: export DSSP=/opt/bin RIGHT: export DSSP=/opt/bin/dssp -Justin Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Friday, November 05, 2010 9:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] dssp Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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 -- 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
RE: [gmx-users] dssp
Last email the paths really look messy, because as I said before, I modified by mine hand before posted it. Sorry about that. I did export the path before. :-) Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: But right now I noticed something a bit funny, Try different times, Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# --- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax /dev/null 2 /dev/null Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k /dev/null 2 /dev/null was something wrong with mine DSSP, except path reason. I still think you're setting your DSSP environment variable wrong. Please consult the link I posted before - you have to point DSSP to the *actual executable* not the directory that contains it, i.e.: WRONG: export DSSP=/opt/bin RIGHT: export DSSP=/opt/bin/dssp -Justin Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Friday, November 05, 2010 9:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] dssp Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA# zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- 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
Re: [gmx-users] dssp
On 6/11/2010 12:57 AM, #ZHAO LINA# wrote: Last email the paths really look messy, because as I said before, I modified by mine hand before posted it. Sorry about that. I did export the path before. :-) People who might spend their time to give free help are not at all interested in things that have been filtered through someone's head. If the contents of the heads were fully correct, then there wouldn't be a problem. Please follow the instructions literally, and report what you did literally when seeking help - that means cut and paste commands and outputs! Mark Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: But right now I noticed something a bit funny, Try different times, Back Off! I just backed up ddbGXXqz to ./#ddbGXXqz.1# --- Program do_dssp, VERSION 4.0.7 Source code file: /home/src/gromacs-4.0.7-mbh/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/zhao0139/src/ball/DSSP/ -na ddbGXXqz ddEflfyy /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddtWJ3ry ddR1Hjkz /dev/null 2 /dev/null Failed to execute command: /home/srcl/DSSP/ -na ddhF6K9M ddcDcvax /dev/null 2 /dev/null Failed to execute command: /home/src/DSSP/ -na ddCFya2b ddJZ2M0k /dev/null 2 /dev/null was something wrong with mine DSSP, except path reason. I still think you're setting your DSSP environment variable wrong. Please consult the link I posted before - you have to point DSSP to the *actual executable* not the directory that contains it, i.e.: WRONG: export DSSP=/opt/bin RIGHT: export DSSP=/opt/bin/dssp -Justin Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of #ZHAO LINA# [zhao0...@e.ntu.edu.sg] Sent: Friday, November 05, 2010 9:35 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] dssp Hi, 1. There is no wrong in mine executable path, it's mine fault that I MODIFIED the real and true path to a simple way as it showed pathTo... before I posted. 2. seems not about root things, cause every body can write and read to/from /dev/null 3. I will try another time ?! Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp Linus Östberg wrote: What did you try to do? To use dssp, you must select entire residues, e.g. 1 (protein). That error sounds a bit like my problem when trying to do dssp using only the backbone. The original message indicates the wrong executable was called. The reasons might still be unclear at this point, but instead of executing dssp, do_dssp was executing pathToDSSP instead. The group for analysis is also debatable. I have seen hangs and seg faults when Protein is selected, and other times it works fine. The only absolute requirement is that (at least) all MainChain atoms be considered. The latest version of GROMACS seems to handle Protein just fine, but older versions did not. I have no explanation for that, however :) -Justin // Linus Östberg On Fri, Nov 5, 2010 at 2:08 PM, #ZHAO LINA#zhao0...@e.ntu.edu.sg wrote: Hi, Thanks for your response, I modified that path parts when I posted that information. So my environment set was correct. I just suddenly realize I may not have root privilege there, cause the dssp was not small, not in mine personal computer, there are in some other places. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 05, 2010 9:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] dssp #ZHAO LINA# wrote: Hi, Program do_dssp, VERSION 4.0.7 Source code file: pathToGromacs/gromacs-4.0.7/src/tools/do_dssp.c, line: 471 Fatal error: Failed to execute command: pathToDSSP/ -na ddEPI6I2 ddFHouPz /dev/null 2 /dev/null It came out two or three file like ddEPI6I2 and then died like above. My first time try dssp, so do not know how to examine it. Your DSSP environment variable is set incorrectly. do_dssp is trying to call pathToDSSP as the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Note that you should substitute a meaningful PATH on your system, not something like pathToDSSP. -Justin Thanks for any advice, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech
[gmx-users] DSSP and g_sas
Which among DSSP and g_sas is better for calculating solvent accessible surface area of proteins? -- Bhanu Prakash. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] DSSP and g_sas
Bhanu Prakash Sandaka wrote: Using DSSP we can also calcuate the surface area, though it doesn't allow changes in probe diameter etc. it does calculate the surface area. I just wish to know whether the performance of DSSP is comparable to g_sas? Should it be used? From do_dssp -h: Note that the program g_sas can also compute SAS and that is more efficient. Otherwise, compare the results, see if one method is better, and read the literature pertaining to SASA calculations to see which method you believe. -Justin -- 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/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/mailing_lists/users.php
Re: [gmx-users] DSSP
Hi Shahid, I have fixed the problem in do_dssp. You can either pull the newest release-4-0-patches branch from the git repository or change ./src/tools/do_dssp.c, line 80 from snew(ssbuf,nres+10); to: snew(ssbuf, 2*nres-1); Carsten On May 19, 2010, at 9:48 AM, Carsten Kutzner wrote: Hi, there was a problem in do_dssp when used on proteins with more than 10 chains. Is this the case? I just saw that I only fixed that in the head, but not in 4.0.x. Carsten On May 18, 2010, at 3:49 PM, shahid nayeem wrote: Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- 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 listgmx-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/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/mailing_lists/users.php -- 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/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
Re: [gmx-users] DSSP
Hi, there was a problem in do_dssp when used on proteins with more than 10 chains. Is this the case? I just saw that I only fixed that in the head, but not in 4.0.x. Carsten On May 18, 2010, at 3:49 PM, shahid nayeem wrote: Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- 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 listgmx-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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe
[gmx-users] DSSP
Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] DSSP
shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- 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/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/mailing_lists/users.php
Re: [gmx-users] DSSP
Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. waiting for your help shahid nayeem On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] DSSP
shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- 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 listgmx-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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php
RE: [gmx-users] DSSP
Shahid, Before trying for do_dssp a gromacs utility calling dssp program , try first dssp program itself by passing simple input like pdb and I hope by that way you can resolve your problem B.Nataraj -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]on Behalf Of shahid nayeem Sent: Tuesday, May 18, 2010 5:17 PM To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] DSSP Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. waiting for your help shahid nayeem On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] DSSP
Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- 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 listgmx-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/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/mailing_lists/users.php -- 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] DSSP
shahid nayeem wrote: Hi When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows. Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time0.000 Warning: if there are broken molecules in the trajectory file, they can not be made whole without a run input file What is your exact command line? -Justin Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1# Segmentation fault shahid On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Hi After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc Other files should be irrelevant. The only file you need is the dssp binary. as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work? Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable. -Justin waiting for your help shahid nayeem On 5/18/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I downloaded dsspcmbi.tar.gz, and compiled using command ./DsspCompileGCC as given in Readme.txt file. when I try to run do_dssp command in gromacs I get error Well, what happened? Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I It won't be there unless you put it there and you have re-named it. I believe the default name of the dssp program is dsspcmbi, which you need to change when you move the executable. http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin even tried dsspcmbi.zip file but again I got the same error. I compiled dssp as root. Now what shoul I do in order to run do_dssp comand of gromacs. Shahid nayeem -- 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/ http://vt.edu/ | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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/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/mailing_lists/users.php -- 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
Re: [gmx-users] dssp problem
pawan raghav wrote: I have download dsspcmbi.zip and extract the dssp folder into /cygdrive/c/cygwin/usr/local/bin/ directory. Then set the environment variable export DSSP=/cygdrive/c/cygwin/usr/local/bin/dssp for bash. then I have gone to my folder by using cd where all my md files were present i.e. /cygdrive/c/gromacs-4.0.7. At last I executed the command do_dssp -f traj.xtc -s md.tpr -n index.ndx -aa area.xvg after preformed this I still got an error i.e. Fatal error: failed to execute command: /cygdrive/c/cygwin/usr/local/bin/dssp ddrN1s8q dd4bcjqa /dev/null 2 /dev/null Please rectify this.. Your environment variable is wrong. If you placed a dssp folder in /usr/local/bin, then the actual executable is located in /usr/local/bin/dssp/dssp. Have a look at the usage notes: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -Justin -- Pawan -- 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/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/mailing_lists/users.php
Re: [gmx-users] dssp FATAL ERROR.
vivek modi wrote: hi, Although this is already discussed in the mailing list but none of the solutions mentioned helped me. I am using Gromacs-4.0.5. I downloaded dssp from http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi Then I copy this to /usr/local/bin chmod to executable. But when I run the program do_dssp it gives the following error: Program do_dssp_4, VERSION 4.0.5 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddXnSQTc ddgMjECf /dev/null 2 /dev/null Any help is appreciated. Did you re-name the executable? Have you set the DSSP environment variable properly? -Justin Thanks. Vivek Modi, Graduate Student, IITK. -- 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/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/mailing_lists/users.php
Re: [gmx-users] DSSP= how to edit .eps file
On 2010-04-04 06.40, Chih-Ying Lin wrote: HI 1. dssp -n index.ndx = only atom numbers of one residue in the index.ndx = can dssp decide the exact second structure for the only one residue without considering other residues of protein? no. = can i get the same second structure for the residue with [ dssp -n one-residue.ndx ] and [dssp -n protein-main chain + H .ndx ] ? no. 2. The legend indicates the color of different second structure is shown under the secondary-structure plot. I don't want to change the colors assigned, but one legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. send your command lines. 3. With the option -sss string HE HE = helix ? no, this is DSSP coding. H = helix , E = extended (Beta sheet), B = beta turn, T = som other kind of turn, 3 = 3-10 heix, 5 = pi helix. Thanks Lin -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] DSSP= how to edit .eps file
Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second structure is shown under the secondary-structure plot. One legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] DSSP= how to edit .eps file
Chih-Ying Lin wrote: Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second structure is shown under the secondary-structure plot. One legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. The dimensions of the plot area are likely too small to accommodate the full legend. As I said before, pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. -Justin Thank you Lin -- 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/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/mailing_lists/users.php
[gmx-users] DSSP= how to edit .eps file
HI How to pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. ??? Thank you Lin Chih-Ying Lin wrote: Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second structure is shown under the secondary-structure plot. One legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. The dimensions of the plot area are likely too small to accommodate the full legend. As I said before, pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. -Justin Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] DSSP= how to edit .eps file
Chih-Ying Lin wrote: HI How to pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. ??? Use the -di flag of xpm2ps. http://manual.gromacs.org/current/online/m2p.html -Justin Thank you Lin Chih-Ying Lin wrote: Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second structure is shown under the secondary-structure plot. One legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. The dimensions of the plot area are likely too small to accommodate the full legend. As I said before, pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. -Justin Thank you Lin -- 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/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/mailing_lists/users.php
Re: [gmx-users] DSSP = how to edit .eps file
Chih-Ying Lin wrote: HI After running DSSP, .eps files are created. No they aren't; you create .eps files from the .xpm output that do_dssp generates. We can see the second structures of the all residues. I only want to see the change of the second structures of some specific residues. How can i do it? As with most (all) Gromacs analysis tools, create an index group for the residues you want to analyze. That will require you to re-run your analysis or otherwise hack your .xpm file (probably not a good idea). Also, how can I change the thickness of the color band for each residue? Use an appropriate .m2p file to alter the attributes of the data. An example is given in the online manual. The logo indicates the color of different second structure is shown not clear for me, how can i make the change on it? Do you want to change the colors assigned, or some other aspect of the legend? You could, in theory, edit the color assignments in the .xpm file. -Justin Thank you Lin -- 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/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/mailing_lists/users.php
Re: [gmx-users] DSSP = how to edit .eps file
On 4/3/10 9:19 PM, Justin A. Lemkul wrote: Chih-Ying Lin wrote: HI After running DSSP, .eps files are created. No they aren't; you create .eps files from the .xpm output that do_dssp generates. We can see the second structures of the all residues. I only want to see the change of the second structures of some specific residues. How can i do it? As with most (all) Gromacs analysis tools, create an index group for the residues you want to analyze. That will require you to re-run your analysis or otherwise hack your .xpm file (probably not a good idea). Also, how can I change the thickness of the color band for each residue? Use an appropriate .m2p file to alter the attributes of the data. An example is given in the online manual. The logo indicates the color of different second structure is shown not clear for me, how can i make the change on it? Do you want to change the colors assigned, or some other aspect of the legend? You could, in theory, edit the color assignments in the .xpm file. With the option -sss string HE you can also choose to show only helix and sheet -Justin Thank you Lin -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] DSSP= how to edit .eps file
HI 1. dssp -n index.ndx = only atom numbers of one residue in the index.ndx = can dssp decide the exact second structure for the only one residue without considering other residues of protein? = can i get the same second structure for the residue with [ dssp -n one-residue.ndx ] and [dssp -n protein-main chain + H .ndx ] ? 2. The legend indicates the color of different second structure is shown under the secondary-structure plot. I don't want to change the colors assigned, but one legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. 3. With the option -sss string HE HE = helix ? Thanks Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] dssp programm
Hello I installed the dssp program for obtaining the secondary structure.I used the dssp programm to analyze the secondary structure of the protein after a MD simulation run. I got the out of the pogramm as m.dssp but I want to know how do I represent the output of the dssp programm graphically or how do I visualize the output of the dssp programm. regards subarna Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] dssp programm
subarna thakur wrote: Hello I installed the dssp program for obtaining the secondary structure.I used the dssp programm to analyze the secondary structure of the protein after a MD simulation run. I got the out of the pogramm as m.dssp but I want to know how do I represent the output of the dssp programm graphically or how do I visualize the output of the dssp programm. If you are using dssp as a standalone executable, you'll just get a text file with some statistics. If you want the nice pictures you see in publications, you have to use do_dssp, which acts as an interface to dssp, and can be used with trajectories. -Justin regards subarna Connect more, do more and share more with Yahoo! India Mail. Learn more http://in.rd.yahoo.com/tagline_galaxy_3/*http://in.overview.mail.yahoo.com/. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
[gmx-users] dssp output of CG structure of 1K4C
Dear all, I wanted to get the dssp output of Coarse Grained structure of my protein i.e. 1K4C. In order to get that I have a script which is given to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully in my linux machine. In my first step i cleaned the 1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG structure using atom2CG script with the help of awk command I get the CG structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it produces the dssp output of my normal cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp output of my CG structure of protein? Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] dssp output of CG structure of 1K4C
sunny mishra wrote: Dear all, I wanted to get the dssp output of Coarse Grained structure of my protein i.e. 1K4C. In order to get that I have a script which is given to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully in my linux machine. In my first step i cleaned the 1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG structure using atom2CG script with the help of awk command I get the CG structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it produces the dssp output of my normal cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp output of my CG structure of protein? Not likely. DSSP calculates secondary structure from hydrogen bonds, which will be absent in a CG model. The script you refer to (dssp2ssd.py) does not use DSSP to calculate secondary structure; it simply converts DSSP output to the .ssd file needed by MARTINI. -Justin Thanks, Sunny ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
