[gmx-users] do_dssp

[Justin A. Lemkul]

Bernhard Knapp wrote:
> The problem with this solution is that I would have to recompile gromacs 
> on all maschines were I want to use dssp, right? Is there an older 
> version of dssp still available from somewhere? On the dssp-homepage I 
> found unfortunatly only the current but no past versions of dssp...
> 

There are indeed old versions on the DSSP homepage (I was unaware of that until 
Mark's reply, which made me poke around).  Under Miscellaneous -> Distribution, 
there is a heading called "DSSPold" that appears to contain the old version of 
the program.

-Justin

> best,
> Bernhard
> 
> 
> 
> Am 04.04.2012 14:03, schrieb gmx-users-request at gromacs.org:
>> Bernhard Knapp wrote:
>>> >  Hi
>>> >  >  I have some problems to get do_dssp running:
>>> >  >  I downloaded the binary of dssp 
>>> fromhttp://swift.cmbi.ru.nl/gv/dssp/  .
>>> >  Then I extracted it using "gunzip dssp-2-linux-i386.gz". Next I 
>>> copied
>>> >  it to the correct location: "cp dssp-2-linux-i386 
>>> /usr/local/bin/dssp"
>>> >  and gave the user the right to execute the binary.
>>> >  If I call dssp in an arbitrary directory (e.g.  "dssp -i test.pdb -o
>>> >  test.dssp") it works fine.  However, if I call it via do_dssp (e.g.
>>> >  "do_dssp -f test.xtc -s test.tpr -o test.xpm") I get the following
>>> >  error: "Fatal error: Failed to execute command: 
>>> /usr/local/bin/dssp -na
>>> >  ddZ2pWoM ddjmIN4j>  /dev/null 2>  /dev/null". If I try to see what is
>>> >  going wrong via executing "/usr/local/bin/dssp -na ddZ2pWoM ddjmIN4j"
>>> >  directly in the shell then I get "unknown option -n".
>>> >  >  Google did not help me since most people who got this error had 
>>> dssp in
>>> >  the wrong path. In my case it definitly finds the executable but 
>>> in the
>>> >  execution something goes wrong ...
>>> >  >  What am I doing wrong?
>>> >  
>> The problem is that the dssp syntax has changed and the Gromacs code 
>> currently
>> can't handle that syntax.  A patch has been proposed in the 
>> development version
>> but it has not yet been incorporated into the git repository.  You 
>> could make
>> the modifications to the source yourself by following:
>>
>> https://gerrit.gromacs.org/#/c/687/
>>
>> -Justin

-- 
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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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