On 4/04/2012 10:02 PM, Justin A. Lemkul wrote:
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/
Or dig around on the dssp site to get the old version.
Mark
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