[gmx-users] Re: gmx-users Digest, Vol 96, Issue 30
bernhard.knapp at meduniwien.ac.at
Wed Apr 4 15:06:53 CEST 2012
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...
Am 04.04.2012 14:03, schrieb gmx-users-request at gromacs.org:
> 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:
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