[gmx-users] Re: gmx-users Digest, Vol 96, Issue 30

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Wed Apr 4 15:06:53 CEST 2012

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...


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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