Bernhard Knapp wrote:
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...
There are indeed old versions on the DSSP homepage (I was unaware of that until
Mark's reply, which made me poke around). Under Miscellaneous -> Distribution,
there is a heading called "DSSPold" that appears to contain the old version of
the program.
-Justin
best,
Bernhard
Am 04.04.2012 14:03, schrieb gmx-users-requ...@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:
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
