[gmx-users] DSSP error
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 10 20:00:18 CET 2010
Justin A. Lemkul wrote:
>
>
> 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.
>
...or check whether or not dssp is actually executable, as I suggested twice before.
-Justin
> -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
>> <mailto:gmx-users-bounces at gromacs.org>>>
>>
>> [gmx-users-bounces at gromacs.org
>> <mailto:gmx-users-bounces at gromacs.org>
>> <mailto:gmx-users-bounces at gromacs.org
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>> <mailto:gmx-users-bounces at gromacs.org
>> <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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