[gmx-users] do_dssp with no output!

Marc Vogt mvogt at es.chem.umass.edu
Thu Mar 18 20:27:00 CET 2004


Did you try specifying the DSSP environment variable? 
I think the default location is /usr/local/bin.


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> Hi all
> I have a problem with the do_dssp module of gromacs: when I run it, after I 
> specify the group (I tried both with "backbone" and with "C-alpha", and 
> it's a 12-aminoacid peptide) the program writes "opening library file 
> /usr/local/share/gromacs/top/ss.map" (the file is there, I checked), then 
> "reading frame 0 time 0.000" "back off! I just backed up " ..... and here 
> it puts strange filenames like "dd0AovgV" and uses all the available CPU 
> without writing the "xpm" file I requested as output. As for these "dd..." 
> files, they look like .gro files for the specified group of my peptide 
> (backbone, or C-alpha).
> The strange thing is that some months ago do_dssp worked perfectly on the 
> same machine, and also on the same trajectory files! (I tried it now on the 
> "old" files to exclude the possibility of problems in the new ones). And, 
> if remember well, when it worked correctly the last line it wrote on screen 
> while running indicated the frame n. it was reading and the corresponding 
> time (updating it), while now this line doesn't appear.
> Referring to the suggestions already made on this mailing list some time 
> ago about a similar problem, I can say that in this case the machine has no 
> disk space problems, and the other gromacs modules run correctly on it.
> Thanks in advance for any suggestion
> Elena
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