[gmx-users] do_dssp

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 4 15:15:34 CEST 2012

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.


> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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