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
As for the path problem, I did it the easy/hard way: I
called dssp from within MATLAB with full filenames
The recommended approach on the dssp webpage,
dsspcmbi source.pdb destination.dssp >messages.txt
doesn't seem to write messages.txt
Post by Dastmalchi
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
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
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.
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.
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