ahmet yıldırım wrote:
Dear Justin, Thanks for your replies
a...@ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb
bash: /usr/local/bin/dssp: cannot execute binary file
That seems to indicate that the dssp executable does not match your
architecture. Get rid of this executable and compile it from source, which I
believe is provided when you download dssp.
-Justin
2010/11/10 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
ahmet yıldırım wrote:
Dear Justin, I don't undertand you said "you haven't chmod +x
dssp)?" Please look at attached photo?
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.
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.
-Justin
Thanks
2010/11/10 Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@vt.edu>>>
ahmet yıldırım wrote:
Hi,
Please tell me which step is wrong:(
1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf
dsspcmbi.tar.gz
2.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi
dssp
3.step-r...@ab-desktop:/home/ab/Desktop/dssp# mv dssp
/usr/local/bin
4.step-r...@ab-desktop:/home/ab/Desktop/dssp# export
DSSP=/usr/local/bin
Your environment variable is wrong. Please read about the proper
way to set it:
http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp
Although, if you've got dssp in /usr/local/bin, that's the
default
location where do_dssp expects it, so there is no need to set the
DSSP environment variable at all.
Perhaps your issue is permission? Or you the dssp executable
isn't
actually executable (i.e., you haven't chmod +x dssp)?
-Justin
5.step...@ab-desktop:~/Desktop/gromacswork$ do_dssp -s
run.tpr
-f run.xtc
Program do_dssp, VERSION 4.0.5
Source code file: ../../../../src/tools/do_dssp.
c, line: 471
*Fatal error:*
Failed to execute command: /usr/local/bin/dssp -na dduigjCp
ddDsSuzR > /dev/null 2> /dev/null
10 Kasım 2010 16:08 tarihinde #ZHAO LINA#
<zhao0...@e.ntu.edu.sg <mailto:zhao0...@e.ntu.edu.sg>
<mailto:zhao0...@e.ntu.edu.sg
<mailto:zhao0...@e.ntu.edu.sg>> <mailto:zhao0...@e.ntu.edu.sg
<mailto:zhao0...@e.ntu.edu.sg>
<mailto:zhao0...@e.ntu.edu.sg
<mailto:zhao0...@e.ntu.edu.sg>>>> yazdı:
http://biskit.pasteur.fr/install/applications/dssp
http://oldwww.gromacs.org/pipermail/gmx-users/2009-April/041004.html
http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp?highlight=dssp
HTH,
lina
------------------------------------------------------------------------
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<mailto:gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>>>] on behalf of ahmet
yıldırım
[ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>
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*Sent:* Wednesday, November 10, 2010 10:02 PM
*To:* Discussion list for GROMACS users
*Subject:* [gmx-users] DSSP error
Hi,
I installed in /usr/local/bin the DSSP program. And I
set the
environment variable with a command such as “export
DSSP=/usr/local/bin/dssp”.
a...@ubuntu:/Desktop/work# do_dssp -s run.tpr -f run.xtc
...
Selected 1: 'Protein'
There are 164 residues in your selected group
Opening library file /usr/share/gromacs/top/ss.map
Reading frame 0 time 0.000 Back Off! I just
backed up dduigjCp to ./#dduigjCp.1#
-------------------------------------------------------
Program do_dssp, VERSION 4.0.5
Source code file: ../../../../src/tools/do_dssp.c,
line: 471
*Fatal error:*
Failed to execute command: /usr/local/bin/dssp -na
dduigjCp
ddDsSuzR
> /dev/null 2> /dev/null
-------------------------------------------------------
"Jesus Not Only Saves, He Also Frequently Makes
Backups." (Myron
Bradshaw)
What should I do?
Thanks in advance
-- Ahmet YILDIRIM
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-- Ahmet YILDIRIM
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Ahmet YILDIRIM
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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