Re: [gmx-users] DSSP configuration in Gromacs 4.5.5
On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DSSP configuration in Gromacs 4.5.5
Dear Sir, Thank u for reply and the old dssp executable was working fine, [root@localhost]# dssp COPYRIGHT W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 CMBI version by elmar.krie...@cmbi.ru.nl / April 1, 2010 USAGE dssp [Options] PDB_File DSSP_File - Read PDB_File and write DSSP_File dssp [Options] -- dssp_file - Read from stdin and write DSSP_File dssp -h - Display this help screen OPTIONS -na Disables the calculation of accessible surface. -cClassic (old) format. -wWide 2002 format (for future use,not the current standard). -vVerbose. --Read from standard input. -h -? Prints a help message. -VPrints version, as in first line of the output. ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS By emmanuel.cource...@toulouse.inra.fr -ssa Adds information about disulfide bonds to output file -xRenames residues with incomplete sidechains to 'X' -alt2 Keeps an additional AltLoc indicator at the line ends [root@localhost]# and i have checked one again the path of DSSP [root@localhost sathish]# echo $DSSP /usr/local/bin/dssp [root@localhost sathish]# but while running with do_dssp has problem. [root@localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx -o ss.xpm :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5-dev-20120318-375fa98 (-: . . . Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Segmentation fault (core dumped) [root@localhost sathish]# Am not clear to understand this problem. help me -- -- Regards, N. Sathishkumar, sath...@khu.ac.kr On Wed, May 16, 2012 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DSSP configuration in Gromacs 4.5.5
On 16/05/2012 5:33 PM, Sathish wrote: Dear Sir, Thank u for reply and the old dssp executable was working fine, [root@localhost]# dssp COPYRIGHT W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 CMBI version by elmar.krie...@cmbi.ru.nl mailto:elmar.krie...@cmbi.ru.nl / April 1, 2010 USAGE dssp [Options] PDB_File DSSP_File - Read PDB_File and write DSSP_File dssp [Options] -- dssp_file - Read from stdin and write DSSP_File dssp -h - Display this help screen OPTIONS -na Disables the calculation of accessible surface. -cClassic (old) format. -wWide 2002 format (for future use,not the current standard). -vVerbose. --Read from standard input. -h -? Prints a help message. -VPrints version, as in first line of the output. ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS By emmanuel.cource...@toulouse.inra.fr mailto:emmanuel.cource...@toulouse.inra.fr -ssa Adds information about disulfide bonds to output file -xRenames residues with incomplete sidechains to 'X' -alt2 Keeps an additional AltLoc indicator at the line ends [root@localhost]# and i have checked one again the path of DSSP [root@localhost sathish]# echo $DSSP /usr/local/bin/dssp [root@localhost sathish]# but while running with do_dssp has problem. [root@localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx -o ss.xpm :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5-dev-20120318-375fa98 (-: You are not using 4.5.5. If you'd shown this the first time, you'd have used less of everybody's time. Maybe this version is one that is updated to use the new DSSP. Maybe you should go and use 4.5.5. Also, don't do routine work logged in as root, unless you like reinstalling your whole operating system. Mark . . . Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Segmentation fault (core dumped) [root@localhost sathish]# Am not clear to understand this problem. help me -- -- Regards, N. Sathishkumar, mailto:sath...@khu.ac.kr On Wed, May 16, 2012 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
