[gmx-users] do_dssp

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Wed Apr 4 12:44:15 CEST 2012


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?


More information about the gromacs.org_gmx-users mailing list