[gmx-users] DSSP error

[Justin A. Lemkul]

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>> 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>
>     [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>]
>     *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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================