[gmx-users] DSSP error

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 10 19:23:21 CET 2010



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
> 
>     ========================================
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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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