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...
best,
Bernhard
Am 04.04.2012 14:03, schrieb [email protected]:
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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