Dear Sir, <br> <br> Thank u for reply and the old dssp executable was working fine, <br><br><br>[root@localhost]# dssp<br>COPYRIGHT<br> W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995<br> CMBI version by <a href="mailto:Elmar.Krieger@cmbi.ru.nl">Elmar.Krieger@cmbi.ru.nl</a> / April 1, 2010<br>
USAGE<br> dssp [Options] PDB_File DSSP_File -> Read PDB_File and write DSSP_File<br> dssp [Options] -- dssp_file -> Read from stdin and write DSSP_File<br> dssp -h -> Display this help screen<br>
OPTIONS<br> -na Disables the calculation of accessible surface.<br> -c Classic (old) format.<br> -w Wide 2002 format (for future use,not the current standard).<br> -v Verbose.<br> -- Read from standard input.<br>
-h -? Prints a help message.<br> -V Prints version, as in first line of the output.<br>ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS<br> By <a href="mailto:Emmanuel.Courcelle@toulouse.inra.fr">Emmanuel.Courcelle@toulouse.inra.fr</a><br>
-ssa Adds information about disulfide bonds to output file<br> -x Renames residues with incomplete sidechains to 'X'<br> -alt2 Keeps an additional AltLoc indicator at the line ends<br>[root@localhost]#<br>
<br><br>
and i have checked one again the path of DSSP<br>
<br>
[root@localhost sathish]# echo $DSSP<br>
/usr/local/bin/dssp<br>
[root@localhost sathish]#<br>
<br>
<br>but while running with do_dssp has problem. <br><br><br>[root@localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx -o ss.xpm<br> :-) G R O M A C S (-:<br><br> Grunge ROck MAChoS<br>
<br> :-) VERSION 4.5.5-dev-20120318-375fa98 (-:<br> . <br> . <br> .<br>Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision)<br>Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision)<br>
Segmentation fault (core dumped)<br>[root@localhost sathish]# <br><br>Am not clear to understand this problem. help me <br><br><br><br>-- <br>-- <br><p style="font-family:arial,helvetica,sans-serif"><font style="font-family:arial,helvetica,sans-serif" size="2">Regards,<br>
N. Sathishkumar,</font></p><br>
<p style="font-family:arial,helvetica,sans-serif"><font><a href="mailto:sathish@khu.ac.kr" target="_blank"><br></a></font></p><br><br><br><br><br><br><br><br><div class="gmail_quote">On Wed, May 16, 2012 at 4:02 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">On 16/05/2012 4:54 PM, Sathish wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all,<br>
<br>
How to install DSSP in Gromacs 4.5.5.<br>
<br>
i set environmental variable "export DSSP=/usr/local/bin/dssp" and checked.<br>
<br>
I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused.<br>
While running i got error " Segmentation fault".<br>
Help me to solve this problem.<br>
</blockquote>
<br></div>
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.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
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</font></span></blockquote></div><br><br clear="all"><br>