[gmx-users] DSSP error
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 10 19:58:19 CET 2010
ahmet yıldırım wrote:
> Dear Justin, Thanks for your replies
>
> ab at 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 <jalemkul at vt.edu <mailto:jalemkul at 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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>>
>
>
>
>
> ahmet yıldırım wrote:
>
> Hi,
>
> Please tell me which step is wrong:(
>
> 1.step-root at ab-desktop:/home/ab/Desktop# tar xvzf
> dsspcmbi.tar.gz
> 2.step-root at ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi
> dssp
> 3.step-root at ab-desktop:/home/ab/Desktop/dssp# mv dssp
> /usr/local/bin
> 4.step-root at 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 at 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#
> <ZHAO0139 at e.ntu.edu.sg <mailto:ZHAO0139 at e.ntu.edu.sg>
> <mailto:ZHAO0139 at e.ntu.edu.sg
> <mailto:ZHAO0139 at e.ntu.edu.sg>> <mailto:ZHAO0139 at e.ntu.edu.sg
> <mailto:ZHAO0139 at e.ntu.edu.sg>
>
> <mailto:ZHAO0139 at e.ntu.edu.sg
> <mailto:ZHAO0139 at 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-bounces at gromacs.org>>>] on behalf of ahmet
> yıldırım
> [ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>
> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>>
> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at gmail.com>
> <mailto:ahmedo047 at gmail.com <mailto:ahmedo047 at 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”.
> ab at 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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> --
> 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> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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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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