[gmx-users] Re: dssp on PC

Christoph Weise cfweise at yahoo.com
Thu Jan 26 15:35:05 CET 2006

One thing I noticed trying out dssp on XP (binary from
http://swift.cmbi.ru.nl/gv/dssp/) is that it is very
quiet so the source of trouble is difficult to trace.
In my case I found some downloaded pdb's were missing
a critical "MODEL" line and dssp was therefore not
returning output.

As for the path problem, I did it the easy/hard way: I
called dssp from within MATLAB with full filenames
including paths.

The recommended approach on the dssp webpage, 

dsspcmbi source.pdb destination.dssp >messages.txt 

doesn't seem to write messages.txt


--- Dastmalchi <dastmalchi.s at tbzmed.ac.ir> wrote:

> Hi,
> DSSP alone is working fine. I did a search in
> Gromacs Search page and
> realized that other people have already raised the
> same problem. Still I
> couldn't find a solution to my problem.
> I have downloaded the dssp for Windows from
> http://swift.cmbi.ru.nl/gv/dssp/.
> I guess do_dssp is not being directed to the
> location of the dssp
> executable. I am not sure but my feeling was that if
> I set the following
> environment variable,
> set dssp=c:\dssp\DSSPCMBI.exe
> and put the dssp directory in the path then issuing
> the dssp command from
> anywhere should locate the executable file.
> Thanks for your kind attention.
> Cheers, Siavoush
> > Hi, Siavoush,
> >
> > It's interesting that my email box did not receive
> your reply until I
> browsed the GMX mailing list today.
> > You may first make sure DSSP works itself, so I
> suggest you carry out DSSP
> to calculate the secondary structure of a known
> structure from PDB databank.
> >
> > Regards,
> >
> > Wang Zhun
> >
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