[gmx-users] DSSP error

[ahmet yıldırım]

Dear Justin, Thanks for your replies

ab at ab-desktop:~/Desktop/gromacswork$ dssp protein.pdb
bash: /usr/local/bin/dssp: cannot execute binary file


2010/11/10 Justin A. Lemkul <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>>
>>
>>
>>
>>
>>    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>>> 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-bounces at gromacs.org
>>        <mailto:gmx-users-bounces at gromacs.org>
>>           <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
>>        <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>>]
>>
>>
>>           *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> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
>>    --     gmx-users mailing list    gmx-users at gromacs.org
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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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-- 
Ahmet YILDIRIM
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