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. -c Classic (old) format. -w Wide 2002 format (for future use,not the current standard). -v Verbose. -- Read from standard input. -h -? Prints a help message. -V Prints 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 -x Renames 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.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 > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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