[gmx-users] do_dssp

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 4 14:02:57 CEST 2012

Bernhard Knapp wrote:
> Hi
> I have some problems to get do_dssp running:
> I downloaded the binary of dssp from http://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:




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


More information about the gromacs.org_gmx-users mailing list