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:
https://gerrit.gromacs.org/#/c/687/
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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