Re: [gmx-users] do_dssp
Preeti, if do_dssp doesn't work for you, try to do it manually using the following web service: http://www.cmbi.ru.nl/hsspsoap/ I use it because my platform (MAC OSX) can't run DO_DSSP Best of luck! On May 14, 2013, at 11:00 AM, Preeti Choudhary preetichoudhary18111...@gmail.com wrote: I am facing problem while using do_dssp.I -- 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] do_dssp
On 5/14/13 11:11 AM, Xu Dong Huang wrote: Preeti, if do_dssp doesn't work for you, try to do it manually using the following web service: http://www.cmbi.ru.nl/hsspsoap/ I use it because my platform (MAC OSX) can't run DO_DSSP I've used dssp/do_dssp on Mac for years. It's all a matter of getting the right binary or installing from source. -Justin -- 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] do_dssp
Hi, I'll try out the 2.1.0 with do_dssp and see if there's something problematic with this new version. Good thing you brought it up. Erik On Mar 1, 2013, at 6:24 PM, Miguel Ángel Mompeán García wrote: Hi Erik, Since I read in the mailing list that nobody had asked about 2.1.0, just decided to try an older version before going into the trouble itself... Kind of coward, I know, but the troubles with that version are already reported so that I thought things would be easier :) Thank-you a lot for your comments 2013/3/1 Erik Marklund er...@xray.bmc.uu.se Interesting. Perhaps there are new issues with 2.1.0. Did you try to execute the command yourself? Erik On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/ null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/ src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/ null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==== 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://vt.edu/Pages/Personal/justin h**ttp://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 htt**p://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/Search h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://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 http://www.gromacs.org/**Support/Mailing_Lists 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-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Search h**ttp://www.gromacs.org/Support/**Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Search before
Re: [gmx-users] do_dssp
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- 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 -- 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] do_dssp
With -ver, just like it says. do_dssp -h explains how. What dssp version do you have? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- 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 -- 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] do_dssp
What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- 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 -- 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] do_dssp
On 3/1/13 11:16 AM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? Supply an .m2p file to xpm2ps -di to adjust the size of each matrix element. There is an example in the online manual. -Justin 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --**- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/**src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==**== 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-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-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-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 thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] do_dssp
Interesting. Perhaps there are new issues with 2.1.0. Did you try to execute the command yourself? Erik On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --**- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/**src/tools/ gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/ null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==**== 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/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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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/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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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/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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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/Search before posting! * Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. * Can't post?
Re: [gmx-users] do_dssp
Hi Erik, Since I read in the mailing list that nobody had asked about 2.1.0, just decided to try an older version before going into the trouble itself... Kind of coward, I know, but the troubles with that version are already reported so that I thought things would be easier :) Thank-you a lot for your comments 2013/3/1 Erik Marklund er...@xray.bmc.uu.se Interesting. Perhaps there are new issues with 2.1.0. Did you try to execute the command yourself? Erik On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote: The issue I mentioned was with dssp-2.1.0. I changed to 2.0.1 and it works fine. However, when converting the xpm to eps I get I plot very small, where one barely can see the colour code and the legend is sooo big. Does anyone know how to change that? 2013/3/1 Erik Marklund er...@xray.bmc.uu.se What happens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD) in your terminal? Erik On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote: I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got: dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1# --- Program do_dssp, VERSION 4.6 Source code file: /usr/local/bin/gromacs-4.6/ src/tools/gmx_do_dssp.c, line: 667 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. How can I fix that? Thanks 2013/1/15 James Starlight jmsstarli...@gmail.com Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- ==== 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://vt.edu/Pages/Personal/justin h**ttp://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 htt**p://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/Search h**ttp://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 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-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Search h**ttp://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
Re: [gmx-users] do_dssp
On 1/15/13 3:19 AM, James Starlight wrote: Dear Gromacs Users! I'd like to know if it's possible to obtain some values from do_dssp except the graph diagrams of the ss dynamics ? For example I wounder to know values of how many residues were in helix, sheet or coil conformation during my simulation ? That's what scount.xvg contains. By the way during analysis of the graph obtained from do_dssp produced by do_dssp -s minim -f md_noPBC.xtc -o ./results/dssp I didnt found legend on the x and y (time, number of residue) as well as color scheme of particular ss element. How I can add it to that graph ? I don't understand what you're asking here. -Justin -- 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] do_dssp
Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 3:19 AM, James Starlight wrote: Dear Gromacs Users! I'd like to know if it's possible to obtain some values from do_dssp except the graph diagrams of the ss dynamics ? For example I wounder to know values of how many residues were in helix, sheet or coil conformation during my simulation ? That's what scount.xvg contains. By the way during analysis of the graph obtained from do_dssp produced by do_dssp -s minim -f md_noPBC.xtc -o ./results/dssp I didnt found legend on the x and y (time, number of residue) as well as color scheme of particular ss element. How I can add it to that graph ? I don't understand what you're asking here. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp
On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- 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] do_dssp
Justin, thanks both options works perfect. James 2013/1/15 Justin Lemkul jalem...@vt.edu: On 1/15/13 7:13 AM, James Starlight wrote: Justin, I want to obtain timescale on X as well as number of residues on Y on the xmp graph . By default that graph has not legend so it's hard to analyse it . The legends are printed in the .xvg header. I've never had a problem plotting its contents (though they are usually somewhat unclear when plotted together) with xmgrace -nxy scount.xvg By the way have you forced with some problems with dppc ? Simetimes I've obtain error like There are 286 residues in your selected group dssp cmd='/usr/local/bin/dssp -i dd42GVbd -o ddpu8ln2 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up dd42GVbd to ./#dd42GVbd.1 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. and I dont know how to fix it. I'm using gromacs-4.6-beta 3 with dssp 2.0.3 Since dssp changed its command line options, Gromacs had to adapt as well. The error tells you to use the -ver option; you should do so. Version 2 should be the default, so check to make sure you're actually using that version and not the old dssp. -Justin -- 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp Segmentation fault
Hello, do_dssp (4.5.5) is broken. There are two possible answers you're gonna get here: 1) Use old dssp, which you are using. 2) You're an idiot, which are not. What I did to solve the problem was, download gmx from git, and substitute the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version. Re-compile it and voila! This do_dssp version accepts both old and new dssp and you have to specify which version with the flag -ver if I remember correctly. This worked perfectly for me. I hope it helps you as well. All the best, João Henriques On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986 mshappy1...@126.com wrote: Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but do_dssp did not work. How can I fix it? Thanks a lot -- 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
Re: [gmx-users] do_dssp Segmentation fault
Hi, The explanation is that DSSP changed its syntax some time ago and do_dssp no longer complied. More recent versions of do_dssp follows the new syntax while still supporting the old one. Erik 12 nov 2012 kl. 10.55 skrev João Henriques: Hello, do_dssp (4.5.5) is broken. There are two possible answers you're gonna get here: 1) Use old dssp, which you are using. 2) You're an idiot, which are not. What I did to solve the problem was, download gmx from git, and substitute the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the git version. Re-compile it and voila! This do_dssp version accepts both old and new dssp and you have to specify which version with the flag -ver if I remember correctly. This worked perfectly for me. I hope it helps you as well. All the best, João Henriques On Mon, Nov 12, 2012 at 8:38 AM, mshappy1986 mshappy1...@126.com wrote: Hi all, I am meeting the following error in Gromacs 4.5.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o dssp.xpm give me the following error segmentation fault I have downloaded the executable DSSP form http://swift.cmbi.ru.nl/gv/dssp/ and set the environment variable, but do_dssp did not work. How can I fix it? Thanks a lot -- 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 --- 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] do_dssp segmental fault
Hi Deb, I recently installed dssp for Gromacs 4.5.4 on RHEL4 You have to just copy the dsspcmbi downloaded from linux distribution to /usr/local/bin (No need to set an environment variable DSSP if dspcmbi is in /usr/loca/bin as it is the default path for gromacs) Rename the dsspcmbi to dssp chmod +x dssp is required if doesn't show as executable. Run do_dssp at any other location. This worked for me. Regards, Archana On Mon, Aug 20, 2012 at 10:49 AM, Debajyoti Ghosh ghosh...@gmail.comwrote: Dear gmx users, I recently upgraded the operating system to Ubuntu 12 and re-installed Gromacs 4.5.5. But I could not re-install dssp. I did the following: (1) I downloaded dsspcmbi from http://swift.cmbi.ru.nl/gv/dssp/ Went to distributions- DSSPold - Linux Distributions to download dsspcmbi. (2) Moved to /usr/local/bin (3) sudo chmod +x dsspcmbi - do_dssp did not work. Then I (a) renamed dsspcmbi to dssp (b) ln -s dsspcmbi dssp - do_dssp still did not work. Then I did : export DSSP=/usr/local/bin/dssp - do_dssp still did not work as well. Please advise. Deb. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 -- Archana Sonawani-Jagtap Junior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp segmentation fault error
On 5/16/12 5:57 AM, bunty xy wrote: Hello Friends I have installed GROMACS 4.5.5 on linux. I put the DSSP Executable in /usr/local/bin when i run the following command: do_dssp -s md.tpr -f md.trr -b 40 -e 50 -o fws_ss.xpm i got the following error. Reading file md.tpr, VERSION 4.5.5 (single precision) Reading file md.tpr, VERSION 4.5.5 (single precision) Segmentation fault Please tell me how can i resolve this Segmentation fault error. This same question was posed just a little bit earlier. You need to make sure you're using the right version of DSSP (the old one). -Justin -- Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp
Bernhard Knapp wrote: Hi I have some problems to get do_dssp running: I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I copied it to the correct location: cp dssp-2-linux-i386 /usr/local/bin/dssp and gave the user the right to execute the binary. If I call dssp in an arbitrary directory (e.g. dssp -i test.pdb -o test.dssp) it works fine. However, if I call it via do_dssp (e.g. do_dssp -f test.xtc -s test.tpr -o test.xpm) I get the following error: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j /dev/null 2 /dev/null. If I try to see what is going wrong via executing /usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j directly in the shell then I get unknown option -n. Google did not help me since most people who got this error had dssp in the wrong path. In my case it definitly finds the executable but in the execution something goes wrong ... What am I doing wrong? The problem is that the dssp syntax has changed and the Gromacs code currently can't handle that syntax. A patch has been proposed in the development version but it has not yet been incorporated into the git repository. You could make the modifications to the source yourself by following: https://gerrit.gromacs.org/#/c/687/ -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
Re: [gmx-users] do_dssp
On 4/04/2012 10:02 PM, Justin A. Lemkul wrote: Bernhard Knapp wrote: Hi I have some problems to get do_dssp running: I downloaded the binary of dssp from http://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I copied it to the correct location: cp dssp-2-linux-i386 /usr/local/bin/dssp and gave the user the right to execute the binary. If I call dssp in an arbitrary directory (e.g. dssp -i test.pdb -o test.dssp) it works fine. However, if I call it via do_dssp (e.g. do_dssp -f test.xtc -s test.tpr -o test.xpm) I get the following error: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j /dev/null 2 /dev/null. If I try to see what is going wrong via executing /usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j directly in the shell then I get unknown option -n. Google did not help me since most people who got this error had dssp in the wrong path. In my case it definitly finds the executable but in the execution something goes wrong ... What am I doing wrong? The problem is that the dssp syntax has changed and the Gromacs code currently can't handle that syntax. A patch has been proposed in the development version but it has not yet been incorporated into the git repository. You could make the modifications to the source yourself by following: https://gerrit.gromacs.org/#/c/687/ Or dig around on the dssp site to get the old version. 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] do_dssp
Bernhard Knapp wrote: The problem with this solution is that I would have to recompile gromacs on all maschines were I want to use dssp, right? Is there an older version of dssp still available from somewhere? On the dssp-homepage I found unfortunatly only the current but no past versions of dssp... There are indeed old versions on the DSSP homepage (I was unaware of that until Mark's reply, which made me poke around). Under Miscellaneous - Distribution, there is a heading called DSSPold that appears to contain the old version of the program. -Justin best, Bernhard Am 04.04.2012 14:03, schrieb gmx-users-requ...@gromacs.org: Bernhard Knapp wrote: Hi I have some problems to get do_dssp running: I downloaded the binary of dssp fromhttp://swift.cmbi.ru.nl/gv/dssp/ . Then I extracted it using gunzip dssp-2-linux-i386.gz. Next I copied it to the correct location: cp dssp-2-linux-i386 /usr/local/bin/dssp and gave the user the right to execute the binary. If I call dssp in an arbitrary directory (e.g. dssp -i test.pdb -o test.dssp) it works fine. However, if I call it via do_dssp (e.g. do_dssp -f test.xtc -s test.tpr -o test.xpm) I get the following error: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j /dev/null 2 /dev/null. If I try to see what is going wrong via executing /usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j directly in the shell then I get unknown option -n. Google did not help me since most people who got this error had dssp in the wrong path. In my case it definitly finds the executable but in the execution something goes wrong ... What am I doing wrong? The problem is that the dssp syntax has changed and the Gromacs code currently can't handle that syntax. A patch has been proposed in the development version but it has not yet been incorporated into the git repository. You could make the modifications to the source yourself by following: https://gerrit.gromacs.org/#/c/687/ -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
Re: [gmx-users] do_dssp segmentation fault
On 3/03/2012 5:14 PM, arun kumar wrote: Dear all, Iam trying to generate secondary structure plot through do_dssp program, but there was an error like segmentation fault Reading file md.tpr, VERSION 4.0.7 (single precision) Reading file md.tpr, VERSION 4.0.7 (single precision) Segmentation fault (core dumped) bash-4.1# can anybody please say what it means and how to solve it No, because there's no diagnostic information. Do other GROMACS tools work? Does the DSSP executable 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] do_dssp segmentation fault
Hi, On Nov 23, 2011, at 8:24 AM, Alex Jemulin wrote: Thanks for your reply Could you tell me the name of the file to download and how to install it? Please follow the instructions at http://www.gromacs.org/Developer_Zone/Git/Basic_Git_Usage and http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial. In short: git clone git://git.gromacs.org/gromacs.git git checkout --track -b release-4-5-patches origin/release-4-5-patches If you are using CMake, you can then just install this like the normal .tar.gz distributions from the gromacs home page. If you are using autotools, do a ./bootstrap before the configure step. Best, Carsten Bests Da: Carsten Kutzner ckut...@gwdg.de A: Alex Jemulin alexbioi...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Inviato: Martedì 22 Novembre 2011 13:25 Oggetto: Re: [gmx-users] do_dssp segmentation fault Dear Alex, On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? I removed a segmentation fault in do_dssp a couple of weeks ago but this is post version 4.5.5. So you need to check out the current release-4-5-patches from the git server. I believe this will fix your problem. Carsten Thank in ad -- 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] do_dssp segmentation fault
On 22/11/2011 7:28 PM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? Make sure you have followed all the instructions available with do_dssp -h, and that your DSSP is the old version, not the updated one. 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] do_dssp segmentation fault
Dear Alex, On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? I removed a segmentation fault in do_dssp a couple of weeks ago but this is post version 4.5.5. So you need to check out the current release-4-5-patches from the git server. I believe this will fix your problem. Carsten Thank in ad -- 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] do_dssp
afsaneh maleki wrote: Hi, I'm trying to use do_dssp of gromacs 4.5.4 in fedora core . I did processes of Download , Uncompress and Compile the source code as the following unzip dsspcmbi.zip cd dssp [root@localhost dssp]# ./DsspCompileGCC That i got this message: Running script to compile the CMBI version of DSSP, please wait... /usr/bin/ld: cannot find -lm collect2: ld returned 1 exit status Type dsspcmbi PDBSourcefile DSSPDestinationfile to run the program... I googled but i don't find clear way to solve this problem. can help me? Really? All the Google results seem to point to the same solution involving installing glibc-devel or some such suitably named package for whatever your system is. Otherwise, contact the DSSP developers so they can tell you the prerequisites. -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
Re: [gmx-users] DO_DSSP
On 6/05/2011 5:22 PM, battis...@libero.it wrote: Dear all, I'm trying install do_dssp on my pc. I followed the steps indicated in the page: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055728.html 1.step-root at ab-desktop:/path-dsspcmbi.tar.gz/# tar xvzf dsspcmbi.tar.gz 2.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp#./DsspCompileGCC 3.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# cp dsspcmbi dssp 4.step-root at ab-desktop:/path-dsspcmbi.tar.gz/dssp# mv dssp /usr/local/bin and the program work well. Now my question: How the program use the file that I downloaded from the web-page: http://swift.cmbi.ru.nl/gv/dssp/ using the indicated instruction? GROMACS doesn't. Read the DSSP documentation about what it is providing. (I found this page from http://www.gromacs.org/Developer_Zone/Programming_Guide/DSSP) rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/ The link rsync://rsync.cmbi.ru.nl/dssp/ is one of the best //database //to calculate the angle into the secondary structures and so to define that, isn't it? One doesn't need a database to calculate angles. 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] do_dssp failed to execute
- Original Message - From: Sunita Patel sun...@mailhost.tifr.res.in Date: Monday, October 11, 2010 22:50 Subject: [gmx-users] do_dssp failed to execute To: Discussion list for GROMACS users gmx-users@gromacs.org Dear User, I set the path for dssp executable in .bashrc file. Still dssp in the path is probably not sufficient. See http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Mark getting following error. Could anybody suggest what would be the problem. error message Select a group: 5 Selected 5: 'MainChain' There are 134 residues in your selected group Opening library file /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading frame 0 time0.000 Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1# --- Program do_dssp, VERSION 4.0.7 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 ddZl9dcf /dev/null 2 /dev/null ** Thanks, Sunit - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp failed to execute
Dear Mark, On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote - Original Message - From: Sunita Patel sun...@mailhost.tifr.res.in Date: Monday, October 11, 2010 22:50 Subject: [gmx-users] do_dssp failed to execute To: Discussion list for GROMACS users gmx-users@gromacs.org Dear User, I set the path for dssp executable in .bashrc file. Still dssp in the path is probably not sufficient. See http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp I already seen this page and the dssp executable file is present in the specified location. I surprise why it was not working before. I freshly downloaded the dsspcmbi executable and rename it to dssp and gave executable file permission and it started working. I was doing like this earlier also. May be dssp executable was corrupted. Thanks, Sunita Mark getting following error. Could anybody suggest what would be the problem. error message Select a group: 5 Selected 5: 'MainChain' There are 134 residues in your selected group Opening library file /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading frame 0 time 0.000 Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1# --- Program do_dssp, VERSION 4.0.7 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 ddZl9dcf /dev/null 2 /dev/null ** Thanks, Sunit - -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. Sunita Patel - Visiting Fellow Department of Chemical Sciences T.I.F.R., Homi Bhabha Road, Colaba Mumbai - 45 - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp failed to execute
Sunita Patel wrote: *** *Dear Mark, On Mon, 11 Oct 2010 22:54:44 +1100, Mark Abraham wrote - Original Message - From: Sunita Patel sun...@mailhost.tifr.res.in Date: Monday, October 11, 2010 22:50 Subject: [gmx-users] do_dssp failed to execute To: Discussion list for GROMACS users gmx-users@gromacs.org Dear User, I set the path for dssp executable in .bashrc file. Still dssp in the path is probably not sufficient. See http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp I already seen this page and the dssp executable file is present in the specified location. I surprise why it was not working before. I freshly downloaded the dsspcmbi executable and rename it to dssp and gave executable file permission and it started working. I was doing like this earlier also. May be dssp executable was corrupted. I would suspect something else was going on. Note from the error message that the dssp executable was not even invoked: Failed to execute command: /home/sunita/soft/bin -na ... Thus, do_dssp was trying to execute bin instead of dssp. The DSSP environment variable must point to the dssp executable itself, not the PATH to it. Maybe you've got things working now, but do check to make sure you've got your environment properly configured to save yourself headaches later. -Justin Thanks, Sunita Mark getting following error. Could anybody suggest what would be the problem. error message Select a group: 5 Selected 5: 'MainChain' There are 134 residues in your selected group Opening library file /home/sunita/soft/gromacs/share/gromacs/top/ss.mapReading frame0 time0.000 Back Off! I just backed up dd3sOJn3 to ./#dd3sOJn3.1# --- Program do_dssp, VERSION 4.0.7 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /home/sunita/soft/bin -na dd3sOJn3 ddZl9dcf /dev/null 2 /dev/null ** Thanks, Sunit - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. Sunita Patel - Visiting Fellow Department of Chemical Sciences T.I.F.R., Homi Bhabha Road, Colaba Mumbai - 45 - -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] do_dssp fatal error
Paymon Pirzadeh wrote: Hello, To investigate the secondary structure I issued the do_dssp command as follows: do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump AFPIII_Ih0001_81_93_NpT265 Then, I had read somewhere in the archive to select the alpha carbons for accurate results, and I did, but the following error pops up: Then you read an inaccurate post. At the very least, all MainChain atoms must be considered. Think about how the DSSP algorithm works - assessment of hydrogen bonding patterns. Can these patterns be determined by using only alpha carbons? I know I have posted several times about how to properly use do_dssp, and it is also on the wiki: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Program do_dssp_d_mpi, VERSION 4.0.5 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na ddOD7WLo ddmJPpUs /dev/null 2 /dev/null The cluster technician tested the forwarded procedure (appended below), and it seems that the backbone structure has some problems. I will be appreciated if one tells me is it really a problem with backbone or sth with installation of dssp. If problem is with backbone, then why pdb2gmx did not issue any warnings? The results below indicate that the command works correctly for groups that contain all the necessary atoms. Failures only occur when other, incorrect, groups are used. -Justin Regards, Paymon Subject: RE: Sorry + Re: GROMACS utilities From: Roman Baranowski ro...@chem.ubc.ca Date: Tue, 5 Oct 2010 19:31:23 -0700 (PDT) To: Paymon Pirzadeh ppirz...@ucalgary.ca To: Paymon Pirzadeh ppirz...@ucalgary.ca Dear Paymon, I have interrupted the run (it was taking too long) and I did not want to prevent you from work in that directory. For: Opening library file /global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat Group 0 ( System) has 293280 elements Group 1 ( Protein) has 1002 elements Group 2 ( Protein-H) has 485 elements Group 3 ( C-alpha) has66 elements Group 4 (Backbone) has 198 elements Group 5 ( MainChain) has 265 elements Group 6 (MainChain+Cb) has 328 elements Group 7 ( MainChain+H) has 327 elements Group 8 ( SideChain) has 675 elements Group 9 ( SideChain-H) has 220 elements Group10 ( Prot-Masses) has 1002 elements Group11 ( Non-Protein) has 292278 elements Group12 ( SOL) has 292278 elements Group13 ( Other) has 292278 elements 0,1,2,5,6,7 work but 3,4,8,9,10,11,12 and 13 do not. However the output Fatal error: Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na ddNPsTyg dda8k3CK suggests that there is some problem with the input. So tried to run dssp -na ddNPsTyg dda8k3CK interactively (without do_dssp_d_mpi -f AFPIII ...) and: dssp -na ddNPsTyg dda8k3CK (I have used the full path i.e.: /global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP) the output is (I remove most of the lines as they do not seem to be relevant): !!! Backbone incomplete for residue ALA1 residue will be ignored !!! !!! Backbone incomplete for residue ASN2 residue will be ignored !!! !!! Backbone incomplete for residue GLN3 residue will be ignored !!! ... .. !!! Backbone incomplete for residue ALA 66 residue will be ignored !!! !!! HEADER-card missing !!! !!! COMPOUND-card missing !!! !!! SOURCE-card missing !!! !!! AUTHOR-card missing !!! !!! No residue with complete backbone !!! So it once again suggests the input issue. I do not know too much about Gromacs and dssp setup but it clearly points to input. All the best Roman On Tue, 5 Oct 2010, Paymon Pirzadeh wrote: Dear Roman, do_dssp does analysis on secondary structure of proteins. It is written on online blogs that to get the correct results, you should select alpha carbons, option 3. However, the only problem that might be the case is providing an index file of backbone alpha carbones which looks irrelevant since do_dssp asks about the group interactively. I don't know if I can try the command or not (since you mentioned it is running), but you may try it again with group option 3. Regards, Paymon On Tue, 2010-10-05 at 16:40 -0700, Roman Baranowski wrote: Dear Paymon, I have just log in as you, cd to: GROMACS/proteins/AFP-III/Ih0001/81_93_204/AFPIII_Ih0001_81_93_NpT265_round1 and issued module load gromacs and than: do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump AFPIII_Ih0001_81_93_NpT265 Select a group: 0 Selected 0: 'System' There are 48779 residues in your selected group Opening library file
Re: [gmx-users] do_dssp fatal error
Dear Justin, Thanks a lot. Your comment was very instructive. So, I use Mainchain (group 5) for future. Paymon On Wed, 2010-10-06 at 12:41 -0400, Justin A. Lemkul wrote: Paymon Pirzadeh wrote: Hello, To investigate the secondary structure I issued the do_dssp command as follows: do_dssp_d_mpi -f AFPIII_Ih0001_81_93_NpT265.xtc -s AFPIII_Ih0001_81_93_NpT265_1.tpr -o AFPIII_Ih0001_81_93_NpT265 -ssdump AFPIII_Ih0001_81_93_NpT265 Then, I had read somewhere in the archive to select the alpha carbons for accurate results, and I did, but the following error pops up: Then you read an inaccurate post. At the very least, all MainChain atoms must be considered. Think about how the DSSP algorithm works - assessment of hydrogen bonding patterns. Can these patterns be determined by using only alpha carbons? I know I have posted several times about how to properly use do_dssp, and it is also on the wiki: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp Program do_dssp_d_mpi, VERSION 4.0.5 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na ddOD7WLo ddmJPpUs /dev/null 2 /dev/null The cluster technician tested the forwarded procedure (appended below), and it seems that the backbone structure has some problems. I will be appreciated if one tells me is it really a problem with backbone or sth with installation of dssp. If problem is with backbone, then why pdb2gmx did not issue any warnings? The results below indicate that the command works correctly for groups that contain all the necessary atoms. Failures only occur when other, incorrect, groups are used. -Justin Regards, Paymon Subject: RE: Sorry + Re: GROMACS utilities From: Roman Baranowski ro...@chem.ubc.ca Date: Tue, 5 Oct 2010 19:31:23 -0700 (PDT) To: Paymon Pirzadeh ppirz...@ucalgary.ca To: Paymon Pirzadeh ppirz...@ucalgary.ca Dear Paymon, I have interrupted the run (it was taking too long) and I did not want to prevent you from work in that directory. For: Opening library file /global/software/gromacs/4.0.5/intel/share/gromacs/top/aminoacids.dat Group 0 ( System) has 293280 elements Group 1 ( Protein) has 1002 elements Group 2 ( Protein-H) has 485 elements Group 3 ( C-alpha) has66 elements Group 4 (Backbone) has 198 elements Group 5 ( MainChain) has 265 elements Group 6 (MainChain+Cb) has 328 elements Group 7 ( MainChain+H) has 327 elements Group 8 ( SideChain) has 675 elements Group 9 ( SideChain-H) has 220 elements Group10 ( Prot-Masses) has 1002 elements Group11 ( Non-Protein) has 292278 elements Group12 ( SOL) has 292278 elements Group13 ( Other) has 292278 elements 0,1,2,5,6,7 work but 3,4,8,9,10,11,12 and 13 do not. However the output Fatal error: Failed to execute command: /global/software/gromacs/dssp/bin/dssp -na ddNPsTyg dda8k3CK suggests that there is some problem with the input. So tried to run dssp -na ddNPsTyg dda8k3CK interactively (without do_dssp_d_mpi -f AFPIII ...) and: dssp -na ddNPsTyg dda8k3CK (I have used the full path i.e.: /global/software/gromacs/dssp/bin/dssp -na ddeqsCnL ddfIOHeP) the output is (I remove most of the lines as they do not seem to be relevant): !!! Backbone incomplete for residue ALA1 residue will be ignored !!! !!! Backbone incomplete for residue ASN2 residue will be ignored !!! !!! Backbone incomplete for residue GLN3 residue will be ignored !!! ... .. !!! Backbone incomplete for residue ALA 66 residue will be ignored !!! !!! HEADER-card missing !!! !!! COMPOUND-card missing !!! !!! SOURCE-card missing !!! !!! AUTHOR-card missing !!! !!! No residue with complete backbone !!! So it once again suggests the input issue. I do not know too much about Gromacs and dssp setup but it clearly points to input. All the best Roman On Tue, 5 Oct 2010, Paymon Pirzadeh wrote: Dear Roman, do_dssp does analysis on secondary structure of proteins. It is written on online blogs that to get the correct results, you should select alpha carbons, option 3. However, the only problem that might be the case is providing an index file of backbone alpha carbones which looks irrelevant since do_dssp asks about the group interactively. I don't know if I can try the command or not (since you mentioned it is running), but you may try it again with group option 3. Regards, Paymon On Tue, 2010-10-05 at 16:40 -0700, Roman Baranowski wrote: Dear Paymon,
Re: [gmx-users] do_dssp
shahid nayeem wrote: Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows. When prompted, what group did you choose for the analysis? -Justin @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend B-Bridge @ s4 legend Bend @ s5 legend Turn @ s6 legend A-Helix @ s7 legend 5-Helix @ s8 legend 3-Helix 04624 0 0 71036 0 3 103926 0 015 435 0 0 203729 0 011 433 0 3 303732 0 011 235 0 0 403631 0 010 630 0 3 504130 0 0 91031 0 0 Please suggest why I am not getting the actual number of residue in dssp file. When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file 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] do_dssp
Hi Justin I choose group 5 main chain for dssp calculation Shahid Nayeem On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows. When prompted, what group did you choose for the analysis? -Justin @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend B-Bridge @ s4 legend Bend @ s5 legend Turn @ s6 legend A-Helix @ s7 legend 5-Helix @ s8 legend 3-Helix 04624 0 0 71036 0 3 103926 0 015 435 0 0 203729 0 011 433 0 3 303732 0 011 235 0 0 403631 0 010 630 0 3 504130 0 0 91031 0 0 Please suggest why I am not getting the actual number of residue in dssp file. When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file 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] do_dssp
shahid nayeem wrote: Hi Justin I choose group 5 main chain for dssp calculation Do you have any capping groups (N-acetyl, C-amine, etc)? -Justin Shahid Nayeem On 5/24/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows. When prompted, what group did you choose for the analysis? -Justin @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend B-Bridge @ s4 legend Bend @ s5 legend Turn @ s6 legend A-Helix @ s7 legend 5-Helix @ s8 legend 3-Helix 04624 0 0 71036 0 3 103926 0 015 435 0 0 203729 0 011 433 0 3 303732 0 011 235 0 0 403631 0 010 630 0 3 504130 0 0 91031 0 0 Please suggest why I am not getting the actual number of residue in dssp file. When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file 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] do_dssp
Hi No i dont have any capping group shahid Nayeem On 5/24/10, Justin A. Lemkul jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I choose group 5 main chain for dssp calculation Do you have any capping groups (N-acetyl, C-amine, etc)? -Justin Shahid Nayeem On 5/24/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Dear All I did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows. When prompted, what group did you choose for the analysis? -Justin @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend B-Bridge @ s4 legend Bend @ s5 legend Turn @ s6 legend A-Helix @ s7 legend 5-Helix @ s8 legend 3-Helix 04624 0 0 71036 0 3 103926 0 015 435 0 0 203729 0 011 433 0 3 303732 0 011 235 0 0 403631 0 010 630 0 3 504130 0 0 91031 0 0 Please suggest why I am not getting the actual number of residue in dssp file. When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file 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] do_dssp
shahid nayeem wrote: Hi No i dont have any capping group Then I have no idea what's going on. The only data that present a problem are in the very first frame, indicating that the HEBT+coil content totals 80 residues. All the other frames look fine. It could be that the algorithm is detecting different structural features for the same residue (i.e., they are somewhat ambiguous), but I have never heard of such an issue. -Justin shahid Nayeem On 5/24/10, *Justin A. Lemkul* jalem...@vt.edu mailto:jalem...@vt.edu wrote: shahid nayeem wrote: Hi Justin I choose group 5 main chain for dssp calculation Do you have any capping groups (N-acetyl, C-amine, etc)? -Justin Shahid Nayeem On 5/24/10, *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 did 10ns simulation of three peptide residue solvated in water. Each peptide residue is 26 residue long. In final .gro file it is showing total 78 residue which is O.K. as 3x26=78. For inserting three similar peptide I used genconf command. when I run dssp I get total residue as 80. The command for dssp is do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the output of dssp run is as follows. When prompted, what group did you choose for the analysis? -Justin @ s0 legend Structure @ s1 legend Coil @ s2 legend B-Sheet @ s3 legend B-Bridge @ s4 legend Bend @ s5 legend Turn @ s6 legend A-Helix @ s7 legend 5-Helix @ s8 legend 3-Helix 04624 0 0 71036 0 3 103926 0 015 435 0 0 203729 0 011 433 0 3 303732 0 011 235 0 0 403631 0 010 630 0 3 504130 0 0 91031 0 0 Please suggest why I am not getting the actual number of residue in dssp file. When I follow the same procedure for full protein molecule simulation I get the same number of residue in dssp output as well as final.gro file 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 -- 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 --
Re: [gmx-users] do_dssp
Do you have a DSSP program on your system? If no, please install executable DSSP program from http://swift.cmbi.kun.nl/gv/dssp/ website. Rasoul On Wed, Jan 6, 2010 at 11:34 AM, leila karami karami.lei...@gmail.comwrote: Hi I apply following command: do_dssp -f rrr.xtc -s .tpr -n n.ndx -map ss.map but following error is came up: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddal9qL4 ddRvmyo0 /dev/null 2 /dev/null Any help will highly appreciated! -- 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] do_dssp
Then your executable has problem. Gromacs tool can not find DSSP for doing d_dssp. Do you put executable DSSP in the path of gromacs is installed? Rasoul. On Wed, Jan 6, 2010 at 11:58 AM, leila karami karami.lei...@gmail.comwrote: dear Rasoul I had executable dssp program, already. leila karami -- 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] do_dssp
On 1/6/10 5:58 AM, leila karami wrote: dear Rasoul I had executable dssp program, already. Then have you set your PATH appropriately, as well as the DSSP environment variable? See the help information for do_dssp to see the assumptions that the program is making regarding the location of the DSSP executable, as well as the numerous posts in the archive about this issue. -Justin leila karami -- 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] do_dssp
On 1/6/10 6:57 AM, rasoul nasiri wrote: Then your executable has problem. Gromacs tool can not find DSSP for doing d_dssp. Do you put executable DSSP in the path of gromacs is installed? This is not necessary. One needs to set the environment variable DSSP correctly, since the default location that do_dssp expects is /usr/local/bin/dssp, not anything to do with the location of Gromacs. -Justin Rasoul. On Wed, Jan 6, 2010 at 11:58 AM, leila karami karami.lei...@gmail.com mailto:karami.lei...@gmail.com wrote: dear Rasoul I had executable dssp program, already. leila karami -- 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/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] do_dssp
On 1/6/10 7:05 AM, leila karami wrote: dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? Is the executable named DSSP, or dssp? Case matters. DSSP is the environment variable that must be set, while dssp is the name of the executable itself. -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] do_dssp
yes. Could you perform do_dssp properly? Rasoul On Wed, Jan 6, 2010 at 1:05 PM, leila karami karami.lei...@gmail.comwrote: dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? -- 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] do_dssp
Hi Leila! Can I add just one more note? The file dssp, that you put in the right place, has the permissions to be executed? Nuno Azoia On Wed, 2010-01-06 at 15:35 +0330, leila karami wrote: dear Rasoul I put executable DSSP in /usr/local/bin and gromacs is in /usr/local/gromacs. is it true? -- 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 -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Têxtil Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt -- 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] do_dssp
On 1/6/10 7:52 AM, leila karami wrote: Hi dear Justin The executable is dssp leila karami Do you have the correct mode set for the executable (i.e., is it actually executable)? Did you use a pre-compiled binary, or compile it yourself from source? If you issue which dssp does your shell find the executable (again going back to potential PATH or environment issues)? -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] do_dssp Installation instructions in case you have errors
Kirill Bessonov wrote: I had seen people having trouble with do_dssp and that Error line 471 error. Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null 2 /dev/null So I would like to spill some light on the issue and make documentation better to understand after hours fiddling with source code. Why did you spend hours looking at the source code? The documentation in do_dssp -h clearly specifies the need to set the executable name in the environment variable DSSP. The documentation and the error message upon non-existence of the path to DSSP could be improved such that it is not specific to C-shell. If you have this error this means that dssp executable was not found even though the PATH was set correctly (i.e. DSSP path variable) It's not a path variable - you've made a wrong assumption. If you look at the source code the fexist funciton checks if there is any file in directory and returns true, so if you have any file there the code will run through and fail on line: sprintf(dssp,%s %s %s %s /dev/null %s, dptr,bDoAccSurf?:-na,pdbfile,tmpfile,bVerbose?:2 /dev/null); where dssp is the buffer of charcters and dptr is the pointer to the dssp executable file (not the folder!) And that is the main source of errors, improper definition of directory pointer to the executable. That's not the mistake. The mistake is GROMACS only checking for existence of the contents of DSSP and assuming the user has read the documentation. If the user erroneously specifies a path which exists, the check succeeds. It could/should check for existence, being executable, not being a directory, being non-zero size, not being a Unix virus, not being an alias for sudo rm -rf /, etc. but one can't protect the user from everything :-) Mark Solution: To correct this mistake add to the path the name of the dssp exectutable. E.g. if you named it dssp and put it in your home folder. Add to .bash_profile DSSP=/home/dssp (where dssp is not a FOLDER but name of executable) If you named executable dsspmbi DSSP=/home/dsspmbi (and again dsspmbi is the name of executable) This will define the location of dssp executable properly and you would not see any weird complicated errors coming up. Hope it helps -- 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] do_dssp question
Kirill Bessonov wrote: I have used do_dssp program to analyze secondary structure during simulation of DMPC/DMPE. But I am not clear on installation of dssp. The program seems to work, I have set all the environmental variables so that dssp binary is seen in /home/DSSP directory, but I am not sure if I need to download the database of dssp files from the internet to make this program work. No libraries or other databases are necessary. There are 14 residues in your selected group Opening library file /usr/local/gromacs/share/gromacs/top/ss.map trn version: GMX_trn_file (single precision) Reading frame 0 time 52.000 Back Off! I just backed up ddoSxMLN to ./#ddoSxMLN.1# Last frame 0 time 52.000 100% And I get ss.xps file that when I open it in image viewer is just a blue line. Then you've got a consistently helical protein. It could be that your axes are skewed a bit, but you can change proportions using a .m2p file. An example is available in the online manual. How should I properly setup the program and whether it will give me %alpha helicity over the course of the trajectory, thank you To calculate % helicity, make use of scount.xvg (the other default output). -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 -- 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
Re: [gmx-users] do_dssp fatal error
Homa Azizian wrote: Hi thanks Dr. van der Spoel my previous problem fixed. I have another question. I download DSSP from http://swift.cmbi.ru.nl/gv/dssp/ from the part Distribution in the left partition of the page. it was the zip file and I unzip it and positioned it in my /usr/local/bin and adjust the .bashrc. when I execut it the error appear: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null 2 /dev/null The executable itself must be in /usr/local/bin. If you placed the unzipped archive in /usr/local/bin, then dssp is a directory. Furthermore, the executable produced from that source code will be call dsspcbmi, and will have to be re-named. -Justin How can I fix the problem? Than's. Tehran University of Medical Sciences www.tums.ac.ir -- Justin A. Lemkul Graduate Research Assistant 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://www.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] do_dssp fatal error
Did you download the dssp software from here ? http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi On Mar 10, 2009, at 1:12 AM, Homa Azizian wrote: Hi when I use do_dssp the following error come: Program do_dssp, VERSION 4.0.3 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null 2 /dev/null How could I fix this. Thank you in advance. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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://www.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] do_dssp
Morteza Khabiri wrote: Dear gmxuser, I ried the do_dssp command to analyses my protein structure. It produce scount.xvg ans ss.xpm file. I could see xvg file by xmgrace and ss,xpm by GIMP software. Till now everything is ok. But when I want a make post script file by xpm2ps for producing plot.eps file I get the following error: There are 1 matrices in ss.xpm Matrix 0 is 954 x 290 Segmentation fault Please be aware a) this has nothing to do with GROMACS (and thus nothing to do with this list), because b) a segmentation fault is an indication of a program failure that can have any conceivable cause, and c) the problem arose in a utility that is not part of GROMACS when the input was known to work in a third-party tool (GIMP). The most likely hypothesis is that your xpm2ps is not suitable for your architecture. If you can test it with some other input, that might give you useful information for diagnosis. The least likely hypothesis is that you've identified a problem in the way GROMACS (in do_dssp) writes a .xpm file. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
Hi, On Wednesday, 29. October 2008, Morteza Khabiri wrote: Dear gmx users, I run the program do_dssp for my system which is too small. Unfortunately, I run it for a long time but I am in a doubt that it is working correctly or not because it is run for one day and i don't have any idea when it will be finished and also after running I have a message which said sh: /usr/local/bin/dssp: is a directory Which take me in a doubt that do_dssp run correctly or not. Please give me at least some idea about end time of program. have you installed dssp? do_dssp -h do_dssp reads a trajectory file and computes the secondary structure for each time frame calling the dssp program. If you do not have the dssp program, get it. do_dssp assumes that the dssp executable is /usr/local/bin/dssp. If this is not the case, then you should set an environment variable DSSP pointing to the dssp executable, e.g.: setenv DSSP /opt/dssp/bin/dssp Greetings, Florian -- --- Dr. Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26573 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
minnale wrote: Hi all, I want to analyse secondary struture of my protein which have run MD for 7ns. I have checked in archives about do_dssp, found that can use only .pdb file instead of .trr and .tpr. Then if type command with -h it has it has given .xtc, .tpr, and .ndx should use. Where does it say that you can't use your trajectory? That's certainly incorrect. The standalone dssp program (which you must obtain separately from the DSSP site) can only run on a single .pdb file, but Gromacs makes use of the dssp executable such that it can be used with trajectories. Hence the lovely plots you see in the literature. -Justin I am bit confusing with about do_dssp command. Can you explain me clearly. Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
As a final note, it is probably better to use the .xtc file for analysis. The do_dssp program is very slow, and I can only imagine that reading the full-precision trajectory will slow to an absolute crawl. -Justin Justin A. Lemkul wrote: minnale wrote: Hi all, I want to analyse secondary struture of my protein which have run MD for 7ns. I have checked in archives about do_dssp, found that can use only .pdb file instead of .trr and .tpr. Then if type command with -h it has it has given .xtc, .tpr, and .ndx should use. Where does it say that you can't use your trajectory? That's certainly incorrect. The standalone dssp program (which you must obtain separately from the DSSP site) can only run on a single .pdb file, but Gromacs makes use of the dssp executable such that it can be used with trajectories. Hence the lovely plots you see in the literature. -Justin I am bit confusing with about do_dssp command. Can you explain me clearly. Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] do_dssp
Thanks for the reply Justin I tried like this do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str it has given Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) I checked with archives do_dssp is a seperate program and install separately, Could you pls tell me how can I install do_dssp program or is there anyway to calculate secondary structure of protein? Thanks in advance. On Fri, 15 Aug 2008 Justin A.Lemkul wrote : As a final note, it is probably better to use the .xtc file for analysis. The do_dssp program is very slow, and I can only imagine that reading the full-precision trajectory will slow to an absolute crawl. -Justin Justin A. Lemkul wrote: minnale wrote: Hi all, I want to analyse secondary struture of my protein which have run MD for 7ns. I have checked in archives about do_dssp, found that can use only .pdb file instead of .trr and .tpr. Then if type command with -h it has it has given .xtc, .tpr, and .ndx should use. Where does it say that you can't use your trajectory? That's certainly incorrect. The standalone dssp program (which you must obtain separately from the DSSP site) can only run on a single .pdb file, but Gromacs makes use of the dssp executable such that it can be used with trajectories. Hence the lovely plots you see in the literature. -Justin I am bit confusing with about do_dssp command. Can you explain me clearly. Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
minnale wrote: Thanks for the reply Justin I tried like this do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str it has given Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) The prerequisite is a separate (non-Gromacs) program called DSSP. It is available here: http://swift.cmbi.ru.nl/gv/dssp/ Install dssp into /usr/local/bin and try do_dssp again. -Justin I checked with archives do_dssp is a seperate program and install separately, Could you pls tell me how can I install do_dssp program or is there anyway to calculate secondary structure of protein? Thanks in advance. On Fri, 15 Aug 2008 Justin A.Lemkul wrote : As a final note, it is probably better to use the .xtc file for analysis. The do_dssp program is very slow, and I can only imagine that reading the full-precision trajectory will slow to an absolute crawl. -Justin Justin A. Lemkul wrote: minnale wrote: Hi all, I want to analyse secondary struture of my protein which have run MD for 7ns. I have checked in archives about do_dssp, found that can use only .pdb file instead of .trr and .tpr. Then if type command with -h it has it has given .xtc, .tpr, and .ndx should use. Where does it say that you can't use your trajectory? That's certainly incorrect. The standalone dssp program (which you must obtain separately from the DSSP site) can only run on a single .pdb file, but Gromacs makes use of the dssp executable such that it can be used with trajectories. Hence the lovely plots you see in the literature. -Justin I am bit confusing with about do_dssp command. Can you explain me clearly. Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
Maybe I can help with some more details. I'm sorry if my explanation is to much detailed. I start to use do_dssp a few days ago. I went to the website Justin just mentioned and I just downloaded the binary file. I copy that file to /usr/local/bin The binary file that I downloaded is dsspcmbi. So, before try do_dssp I create a soft link dssp to the binary dsspcmbi. I've created the link in the same directory (/usr/local/bin), and everything is just work fine. Nuno Azoia Justin A. Lemkul wrote: minnale wrote: Thanks for the reply Justin I tried like this do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str it has given Fatal error: DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP) The prerequisite is a separate (non-Gromacs) program called DSSP. It is available here: http://swift.cmbi.ru.nl/gv/dssp/ Install dssp into /usr/local/bin and try do_dssp again. -Justin I checked with archives do_dssp is a seperate program and install separately, Could you pls tell me how can I install do_dssp program or is there anyway to calculate secondary structure of protein? Thanks in advance. On Fri, 15 Aug 2008 Justin A.Lemkul wrote : As a final note, it is probably better to use the .xtc file for analysis. The do_dssp program is very slow, and I can only imagine that reading the full-precision trajectory will slow to an absolute crawl. -Justin Justin A. Lemkul wrote: minnale wrote: Hi all, I want to analyse secondary struture of my protein which have run MD for 7ns. I have checked in archives about do_dssp, found that can use only .pdb file instead of .trr and .tpr. Then if type command with -h it has it has given .xtc, .tpr, and .ndx should use. Where does it say that you can't use your trajectory? That's certainly incorrect. The standalone dssp program (which you must obtain separately from the DSSP site) can only run on a single .pdb file, but Gromacs makes use of the dssp executable such that it can be used with trajectories. Hence the lovely plots you see in the literature. -Justin I am bit confusing with about do_dssp command. Can you explain me clearly. Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null -- Nuno Gonçalo Azoia Lopes Laboratório de Investigação em Acabamento Departamento de Engenharia Têxtil Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp file format
ABEL Stephane 175950 wrote: Hi Gromacs users After many try this weekend with my problem with do_dssp I come back to the mailing list First, as David said me last friday in a previous message I have test my dssp program with example of pdb file from the Protein Data Bank (1HRC) (with one protein configuration in it) It works ! the calculation of the secondary structure is made and i obtain an output. When i use this pdb with do_dssp with the following command /applications/gromacs-3.3.2-fftw/bin/do_dssp -s test_template.pdb -f test_template.pdb -o ss.xpm I obtain the menu and I choose 5 (MainChain) I obtained the follwing message: There are 103 residues in your selected group Opening library file /applications/gromacs-3.3.2-fftw/share/gromacs/top/ss.map Reading frame 0 time -1.000 Back Off! I just backed up ddEG4D6s to ./#ddEG4D6s.1# And the calculation is not made (I wait more than ten minutes) and i obtain no ss.xpm I dont understand what is the problem This could easily be too short a time if there are multiple frames in your pdb file. I don't know whether you have or need to follow the suggestion I made last time... http://www.gromacs.org/pipermail/gmx-users/2008-January/031720.html Also, per man do_dssp you need to have set your DSSP environment variable correctly. Finally, test do_dssp on the same .pdb file you say works with dssp. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp file format
Quoting ABEL Stephane 175950 [EMAIL PROTECTED]: My story with do_dssp continues...https://webmail.cea.fr/Exchange/Stephane.ABEL/Bo%C3%AEte%20de%20r%C3%A9ception/?Cmd=contentsPage=1 Boîte de réception As suggested David and others i rename my pdb file with the extension .pdb i used the following command ./do_dssp -s RM106-Cytc-CH22-SecStruc.pdb -f RM106-Cytc-CH22-SecStruc.pdb A menu appears, I choose the group 1 (protein) and i obtained the error message Opening library file /applications/gromacs-3.2.1/share/top/ss.map Reading frame 0 time -1.000 Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# What iis the problem. I give below a part of my pdb file I don't see any error message. But you're not going to get any output that way. As I (and others) have posted to the list several times, use the group 'MainChain' for secondary structure calculations. Check the archive for these things, the answers are often there. -Justin ATOM 1 CAY ACE 1 6.421 -7.877 -11.574 -0.27 0.00 ATOM 2 HA1 ACE 1 6.050 -8.804 -12.062 0.09 0.00 ATOM 3 HA2 ACE 1 6.728 -7.203 -12.402 0.09 0.00 ATOM 4 HA3 ACE 1 5.529 -7.417 -11.098 0.09 0.00 ATOM 5 CACE 1 7.470 -8.140 -10.510 0.51 0.00 ATOM 6 OACE 1 7.594 -9.280 -10.074 -0.51 0.00 ATOM 7 NGLY 2 8.125 -7.096 -10.030 -0.47 0.00 ATOM 8 HN GLY 2 7.927 -6.156 -10.295 0.31 0.00 ATOM 9 CA GLY 2 8.970 -7.131 -8.819 -0.02 0.00 ATOM 10 HA1 GLY 2 8.889 -8.007 -8.193 0.09 0.00 ATOM 11 HA2 GLY 2 8.638 -6.265 -8.265 0.09 0.00 ATOM 12 CGLY 2 10.408 -6.734 -9.033 0.51 0.00 ATOM 13 OGLY 2 11.313 -7.365 -8.492 -0.51 0.00 ATOM 14 NASP 3 10.647 -5.532 -9.599 -0.47 0.00 ATOM 15 HN ASP 3 9.863 -5.073 -10.011 0.31 0.00 ATOM 16 CA ASP 3 11.864 -4.806 -9.831 0.07 0.00 ATOM 17 HA ASP 3 12.713 -5.321 -9.406 0.09 0.00 ATOM 18 CB ASP 3 12.026 -4.347 -11.282 -0.28 0.00 ATOM 19 HB1 ASP 3 11.065 -4.008 -11.725 0.09 0.00 ATOM 20 HB2 ASP 3 12.877 -3.652 -11.448 0.09 0.00 ATOM 21 CG ASP 3 12.414 -5.579 -12.163 0.62 0.00 ATOM 22 OD1 ASP 3 11.641 -5.923 -13.130 -0.76 0.00 ATOM 23 OD2 ASP 3 13.571 -5.997 -12.137 -0.76 0.00 Thank you again for your kindly help Stefane ABEL Stephane 175950 wrote: I used the following command ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinates of my MD. don't rename the .pdb file to .tpr. Just use .pdb -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- Message: 2 Date: Fri, 11 Jan 2008 09:30:47 +1100 From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Kirk wrote: Mark Abraham [EMAIL PROTECTED] wrote Non-Protein serves well here. So a usual tc-grps line has Protein Non-Protein for a protein simulation. Mark A supplementary question. The tc-grps line can take predefined standard group names such as 'System', 'Protein' and 'Non-Protein'. Does the 'Protein' group need to actually BE a protein, or are 'Protein' and 'Non-Protein' really synonyms for 'PresumablyBigMoleculeOfInterestProteinOrNot' and 'EverythingElse' ? I haven't read the code or found any mention in the manual, but I expect that src/share/top/aminoacids.dat contains the names of any amino acids, and thus implicitly defines these groups. Mark -- Message: 3 Date: Fri, 11 Jan 2008 09:24:40 +0800 From: xuji[EMAIL PROTECTED] Subject: [gmx-users] Asking help about PME To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=gb2312 Hi all gromacs users: I am digging into the PME method in gromacs. Can someone tell me what files have something to do with PME and the corresponding method FFT? Thanks! Best wishes! Ji Xu Institute of Process Engineering Chinese Academy of Sciences P.O.Box 353, Beijing, 100080, China Tel: +86-10-82627076 Fax:+86-10-62558065 [EMAIL PROTECTED] 2008-01-11 -- next part --
Re: [gmx-users] do_dssp file format
ABEL Stephane 175950 wrote: I am back :( The procedure i did 1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm The menu appears I choose 5 (Main Chain) and I obtained the following message try running normal dssp first dssp pdbfile to see if dssp works -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp file format
Is it a single structure in the .pdb file? Or is it many frames of a trajectory? It is noted in the manual that do_dssp is very slow. In my experience (on my laptop), I can analyze 5 frames in roughly 3 hours. Are you waiting long enough for do_dssp to finish? -Justin Quoting ABEL Stephane 175950 [EMAIL PROTECTED]: I am back :( The procedure i did 1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm The menu appears I choose 5 (Main Chain) and I obtained the following message GROningen MAchine for Chemical Simulation :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /applications/gromacs-3.3.1-fftw/bin/do_dssp (-: Option Filename Type Description -f test-Struc.pdb InputGeneric trajectory: xtc trr trj gro g96 pdb -s test-Struc.pdb InputStructure+mass(db): tpr tpb tpa gro g96 pdb xml -n index.ndx Input, Opt. Index file -ssdump ssdump.dat Output, Opt. Generic data file -map ss.map Input, Lib. File that maps matrix data to colors -o ss.xpm Output X PixMap compatible matrix file -sc scount.xvg Output xvgr/xmgr file -a area.xpm Output, Opt. X PixMap compatible matrix file -tatotarea.xvg Output, Opt. xvgr/xmgr file -aa averarea.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]X bool no Use dialog box GUI to edit command line options -niceint 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 1 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: ps, fs, ns, us, ms or s -[no]w bool no View output xvg, xpm, eps and pdb files -[no]xvgr boolyes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -sss string HEBT Secondary structures for structure count Opening library file /applications/gromacs-3.3.1-fftw/share/gromacs/top/phbres.dat Opening library file /applications/gromacs-3.3.1-fftw/share/gromacs/top/aminoacids.dat Group 0 ( System) has 1674 elements Group 1 ( Protein) has 1623 elements Group 2 ( Protein-H) has 796 elements Group 3 ( C-alpha) has 101 elements Group 4 (Backbone) has 304 elements Group 5 ( MainChain) has 405 elements Group 6 (MainChain+Cb) has 494 elements Group 7 ( MainChain+H) has 405 elements Group 8 ( SideChain) has 1218 elements Group 9 ( SideChain-H) has 391 elements Group10 ( Prot-Masses) has 1623 elements Group11 ( Non-Protein) has51 elements Group12 ( HSD) has51 elements Group13 ( Other) has51 elements I select a group: 5 Selected 5: 'MainChain' There are 102 residues in your selected group --- OK for me Opening library file /applications/gromacs-3.3.1-fftw/share/gromacs/top/ss.map Reading frame 0 time -1.000 Back Off! I just backed up ddsGGvys to ./#ddsGGvys.1# The ddsGGvys is indeed a pdb file with the protein atoms (main chain). But the program seems to run because the prompt did not appear but the ouput ss.xpm is never present. What is the problem ? Thank you Thanks Justin for your reply So I used the choice 5(MainChain), 6(MainChain+Cb) and 7(MainChain+H)to test. I obtained always the same error. Opening library file /applications/gromacs-3.2.1/share/top/ss.map Reading frame 0 time -1.000 Back Off! I just backed up ddjapK9A to ./#ddjapK9A.1# What error? It appears that do_dssp is backing up an old intermediate file that gets generated as part of the calculation. -Justin Note that the pdb seems correct because the secondary structure can be obtained with Stride available in VMD. And my trajectory was made CHARMM ffield. is this a problem in this case Thank a lot My story with do_dssp As suggested David and others i rename my pdb file with the extension .pdb i used the following command ./do_dssp
Re: [gmx-users] do_dssp file format
ABEL Stephane 175950 wrote: I am back :( The procedure i did 1) do_dssp -s test-Struc.pdb -f test-Struc.pdb -dt 1 -o ss.xpm The menu appears I choose 5 (Main Chain) and I obtained the following message The ddsGGvys is indeed a pdb file with the protein atoms (main chain). But the program seems to run because the prompt did not appear but the ouput ss.xpm is never present. What is the problem ? http://wiki.gromacs.org/index.php/do_dssp Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp file format
Quoting ABEL Stephane 175950 [EMAIL PROTECTED]: Hi gromacs users For my work I have performed some simulations of a protein in water with an other MD software not compatible with GROMACS. And I would like to compute the time evolution of the secondary structure of my protein, I know that the with the xpm2ps tool give in gromacs. Is it possible to have an (small) exemple of an .xpm file generated by the do_dssp tools Just run a 10-step MD simulation and generate one yourself. Or convert your other trajectories into .pdb format and use that as input to do_dssp. You do not necessarily need a .tpr file for do_dssp, see man do_dssp under the -s flag. Mark Thanks Mark for your suggestions but it is not working for me So i have tested an other approach with VMD to obtain the secondary structure time series for my protein. The ouput graph obtained is not pretty, so i would like to make for a paper a same graph that i found in some gromacs papers. For this i need to convert the output datas file of VMD to gromacs xpm file obtained with do_dssp with a script and convert it to ps with the xpm2ps tool. In gromacs documentation i can not find an exemple of xpm file generated with do_dssp. So it is possible to obtain from the gromacs users a small exemple of this file to see how the datas are arranged What exactly is not working? As in, what commands are you issuing? Did the MD fail, or the analysis of the trajectory? If you provide this type of information, we may be able to help you better. -Justin Thank you very much Stefane ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp file format
ABEL Stephane 175950 wrote: I used the following command ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinates of my MD. don't rename the .pdb file to .tpr. Just use .pdb -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp file format
ABEL Stephane 175950 wrote: Hi gromacs users For my work I have performed some simulations of a protein in water with an other MD software not compatible with GROMACS. And I would like to compute the time evolution of the secondary structure of my protein, I know that the do_dssp tool in GROMACS is made for this. This tools also plot the results in .xpm matrix file which can be convert with the xpm2ps tool give in gromacs. Is it possible to have an (small) exemple of an .xpm file generated by the do_dssp tools Just run a 10-step MD simulation and generate one yourself. Or convert your other trajectories into .pdb format and use that as input to do_dssp. You do not necessarily need a .tpr file for do_dssp, see man do_dssp under the -s flag. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp for many peptides
Volker Knecht wrote: Dear all, Does anyone have an idea what is going wrong? No, but it would straightforward to write a script that used trjconv while iterating through a set of index files that extract the coordinates of just one peptide at a time, write that to an intermediate .xtc file and send that to do_dssp individually. There's no chemical reason to want do_dssp to do this looping for you, and you may discover the source of the problem if/when this manual loop breaks. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp: main chain
Hi, perhaps your .trr has some errors. Have you tried converting it or gmxcheck? Other solution could be: Transfer your protein residues to an multiple pdb file and try do_dssp again. Perhaps your top or ndx doesn't fit. On Wednesday, 23. May 2007 17:07, Volker Knecht wrote: Dear all, Message: 4 Date: Wed, 23 May 2007 10:16:59 -0400 From: Justin Lemkul [EMAIL PROTECTED] Subject: Re: [gmx-users] Re: Re: do_dssp for many peptides To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 do_dssp claims that are 248 residues in my selected group, although 248 is the number of *atoms* (not of residues) of this peptide. After the notion that some temporary file is backed up, do_dssp gets stuck again. I have even tried exactly Mark's suggestion (xtc file containing single peptide) for test reasons, but a similar problem occurs for the peptide denoted as chain N: do_dssp claims that are 124 residues in my selected group, although 124 is the number of *atoms* (not of residues) of this peptide. After the notion that some temporary file is backed up, do_dssp gets stuck again. I saw a similar description in the archives a long time ago when I was looking for help on do_dssp and experiencing similar problems (with a simpler system, granted). Which group are you selecting for running do_dssp? These errors seem to come up if you select any group other than 'MainChain' (choice 5, I believe). If do_dssp is finding an incorrect number of residues, perhaps you have selected 'Protein' instead of 'MainChain' for your analysis? Thanks for your reply, Justin. Indeed I had chosen 'Protein' so far. But it is not evident that this caused the problem, since it worked well in some cases. Indeed, choosing 'MainChain' (indeed index group 5) does not help, but results in the same behavior. Volker Greetings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp crashes on certain machines..
[EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Do the analysis piecewise... trjconv to break the .trr into chunks, and now you can even do the analysis in parallel. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp crashes on certain machines..
hi, On Thursday, 19. April 2007 17:23, Mark Abraham wrote: [EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Do the analysis piecewise... trjconv to break the .trr into chunks, and now you can even do the analysis in parallel. Could be a nice application for pushing parallel filesystems to its limits! Perhaps it could be implemented in upcoming gromacs versions, something like mpich wrapper for certain analysis tools. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Grettings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp
singh wrote: Dear Gromacs users, As I am simulating many peptides in a box and do_dssp is only a wrapper for calling the program which works on pdb files, I was of the view that it will not take PBC into consideration and will probably not assign beta sheets very well. Please correct me if I am wrong. If this is the case, Is there any other way to assign secondary structure to such a system? many programs do that, e.g. pymol, or VMD, but you have to verify for yourself. dssp does not take PBC into account. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp error
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jahan, First, you must make sure you have the dssp program; it doesn't come with gromacs, but you can download it separately from: http://swift.cmbi.ru.nl/gv/dssp/ Secondly, if 'setenv' is not working you are not on a csh/tcsh shell. Try: export DSSP=/path_to_your_dssp_installation/dssp This should work if you are on a sh/bash shell. HTH, Miguel jahanshah ashkani wrote: Hi, I have a problem with do_dssp command. When I ran it, I found this fatal error ? DSSP executable /usr/local/bin/dssp does not exist. Then I used from setenv DSSP command, but I found this error ?setenv is not recognized as an internal or external command,..? I would be glad if you help me in this case. Thank you very much. Sincerely yours, Jahan Yahoo! Messenger with Voice. Make PC-to-Phone Calls http://us.rd.yahoo.com/mail_us/taglines/postman1/*http://us.rd.yahoo.com/evt=39663/*http://voice.yahoo.com to the US (and 30+ countries) for 2¢/min or less. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.ysbl.york.ac.uk/~mol/ ~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFEUHCSF6oOrDvhbQIRAszAAJ9qofxtTpvwqYZcKYmUFzoyy6/uJgCePeiu LzKSZcKBbttCO+r6pU5Uy6E= =jweu -END PGP SIGNATURE- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] do_dssp error
Thanks for your reply. I used from Gromacs on WindowsXP with command prompt. How can I change DSSP path in this environment? Thank you very much.Sincerely yours, JahanMiguel Ortiz Lombardia [EMAIL PROTECTED] wrote: -BEGIN PGP SIGNED MESSAGE-Hash: SHA1Hi Jahan,First, you must make sure you have the dssp program; it doesn't comewith gromacs, but you can download it separately from:http://swift.cmbi.ru.nl/gv/dssp/Secondly, if 'setenv' is not working you are not on a csh/tcsh shell. Try:export DSSP=/path_to_your_dssp_installation/dsspThis should work if you are on a sh/bash shell.HTH,Migueljahanshah ashkani wrote: Hi, I have a problem with do_dssp command. When I ran it, I found this fatal error ? DSSP executable does not exist. Then I used from setenv DSSP command, but I found this error ?setenv is not recognized as an internal or external command,..? I would be glad if you help me in this case. Thank you very much. Sincerely yours, Jahan Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less. ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php- --Miguel Ortiz LombardíaCentro de Investigaciones OncológicasC/ Melchor Fernández Almagro, 328029 Madrid, SpainTel. +34 912 246 900Fax. +34 912 246 976email: [EMAIL PROTECTED]www: http://www.ysbl.york.ac.uk/~mol/~~~Je suis de la mauvaise herbe,Braves gens, braves gens,Je pousse en libertéDans les jardins mal fréquentés!Georges Brassens-BEGIN PGP SIGNATURE-Version: GnuPG v1.4.1 (GNU/Linux)iD8DBQFEUHCSF6oOrDvhbQIRAszAAJ9qofxtTpvwqYZcKYmUFzoyy6/uJgCePeiuLzKSZcKBbttCO+r6pU5Uy6E==jweu-END PGP SIGNATURE-___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php New Yahoo! Messenger with Voice. Call regular phones from your PC and save big.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
