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On 16/05/2012 5:33 PM, Sathish wrote:
<blockquote
cite="mid:CAEEjrtsuQqOdVr39E9SZvLR5qVyRwqNwdhqU9UxkMUcAKBA3JQ@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
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 moz-do-not-send="true"
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>
</blockquote>
<br>
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.<br>
<br>
Also, don't do routine work logged in as root, unless you like
reinstalling your whole operating system.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEEjrtsuQqOdVr39E9SZvLR5qVyRwqNwdhqU9UxkMUcAKBA3JQ@mail.gmail.com"
type="cite"> . <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
moz-do-not-send="true" 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 moz-do-not-send="true"
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>
-- <br>
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</font></span></blockquote>
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