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>> 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
------------------------------------------------------------------------
*From:* gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
[gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>] on behalf of ahmet yıldırım
[ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>]
*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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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