Dear Justin, Thanks for your replies<br><br>ab@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb<br>bash: /usr/local/bin/dssp: cannot execute binary file<br><br><br><div class="gmail_quote">2010/11/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
ahmet yıldırım wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Justin, I don't undertand you said "you haven't chmod +x dssp)?" Please look at attached photo?<br>
<br>
</blockquote>
<br></div>
I guess that means it's executable; I'm not used to looking into things with the filesystem browser window. I just couldn't remember if the dssp executable was, by default, capable of being executed. The command in the terminal would be what I quoted before.<br>
<br>
Do a test: can you run the dssp executable on a .pdb file? That is, don't call it via do_dssp, try to use it in its standalone capacity.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks<br>
<br>
<br>
2010/11/10 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><div></div><div class="h5">
<br>
<br>
<br>
<br>
ahmet yıldırım wrote:<br>
<br>
Hi,<br>
<br>
Please tell me which step is wrong:(<br>
<br>
1.step-root@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz<br>
2.step-root@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp<br>
3.step-root@ab-desktop:/home/ab/Desktop/dssp# mv dssp /usr/local/bin<br>
4.step-root@ab-desktop:/home/ab/Desktop/dssp# export<br>
DSSP=/usr/local/bin<br>
<br>
<br>
Your environment variable is wrong. Please read about the proper<br>
way to set it:<br>
<br>
<br>
<a href="http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp" target="_blank">http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp</a><br>
<br>
Although, if you've got dssp in /usr/local/bin, that's the default<br>
location where do_dssp expects it, so there is no need to set the<br>
DSSP environment variable at all.<br>
<br>
Perhaps your issue is permission? Or you the dssp executable isn't<br>
actually executable (i.e., you haven't chmod +x dssp)?<br>
<br>
-Justin<br>
<br>
5.step-ab@ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr<br>
-f run.xtc<br>
<br>
Program do_dssp, VERSION 4.0.5<br>
Source code file: ../../../../src/tools/do_dssp.<br>
c, line: 471<br>
<br>
*Fatal error:*<br>
Failed to execute command: /usr/local/bin/dssp -na dduigjCp<br>
ddDsSuzR > /dev/null 2> /dev/null<br>
<br>
<br>
<br>
<br>
10 Kasım 2010 16:08 tarihinde #ZHAO LINA# <<a href="mailto:ZHAO0139@e.ntu.edu.sg" target="_blank">ZHAO0139@e.ntu.edu.sg</a><br></div></div>
<mailto:<a href="mailto:ZHAO0139@e.ntu.edu.sg" target="_blank">ZHAO0139@e.ntu.edu.sg</a>> <mailto:<a href="mailto:ZHAO0139@e.ntu.edu.sg" target="_blank">ZHAO0139@e.ntu.edu.sg</a><div class="im"><br>
<mailto:<a href="mailto:ZHAO0139@e.ntu.edu.sg" target="_blank">ZHAO0139@e.ntu.edu.sg</a>>>> yazdı:<br>
<br>
<br>
<a href="http://biskit.pasteur.fr/install/applications/dssp" target="_blank">http://biskit.pasteur.fr/install/applications/dssp</a><br>
<br>
<a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html" target="_blank">http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html</a><br>
<br>
<a href="http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp" target="_blank">http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp</a><br>
<br>
HTH,<br>
<br>
lina<br>
------------------------------------------------------------------------<br>
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<mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>>>] on behalf of ahmet yıldırım<br>
[<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a> <mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>><br></div>
<mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a> <mailto:<a href="mailto:ahmedo047@gmail.com" target="_blank">ahmedo047@gmail.com</a>>>]<div><div></div><div class="h5">
<br>
<br>
*Sent:* Wednesday, November 10, 2010 10:02 PM<br>
*To:* Discussion list for GROMACS users<br>
*Subject:* [gmx-users] DSSP error<br>
<br>
Hi,<br>
<br>
I installed in /usr/local/bin the DSSP program. And I set the<br>
environment variable with a command such as “export<br>
DSSP=/usr/local/bin/dssp”.<br>
ab@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc<br>
...<br>
Selected 1: 'Protein'<br>
There are 164 residues in your selected group<br>
Opening library file /usr/share/gromacs/top/ss.map<br>
Reading frame 0 time 0.000 Back Off! I just<br>
backed up dduigjCp to ./#dduigjCp.1#<br>
<br>
-------------------------------------------------------<br>
Program do_dssp, VERSION 4.0.5<br>
Source code file: ../../../../src/tools/do_dssp.c, line: 471<br>
<br>
*Fatal error:*<br>
Failed to execute command: /usr/local/bin/dssp -na dduigjCp<br>
ddDsSuzR<br>
> /dev/null 2> /dev/null<br>
-------------------------------------------------------<br>
"Jesus Not Only Saves, He Also Frequently Makes Backups." (Myron<br>
Bradshaw)<br>
<br>
What should I do?<br>
<br>
Thanks in advance<br>
<br>
-- Ahmet YILDIRIM<br>
<br>
--<br>
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-- Ahmet YILDIRIM<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div><div></div><div class="h5"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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-- <br>
Ahmet YILDIRIM<br>
<br>
------------------------------------------------------------------------<br>
<br>
</div></div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Ahmet YILDIRIM<br>