ABEL Stephane 175950 wrote:
Hi Gromacs users
After many try this weekend with my problem with do_dssp I come back to the mailing list
First, as David said me last friday in a previous message I have test my dssp
program with example of pdb file from the Protein Data Bank (1HRC) (with one
protein configuration in it)
It works ! the calculation of the secondary structure is made and i obtain an output.
When i use this pdb with do_dssp with the following command
/applications/gromacs-3.3.2-fftw/bin/do_dssp -s test_template.pdb -f test_template.pdb -o ss.xpm
I obtain the menu and I choose 5 (MainChain)
I obtained the follwing message:
There are 103 residues in your selected group
Opening library file /applications/gromacs-3.3.2-fftw/share/gromacs/top/ss.map
Reading frame 0 time -1.000
Back Off! I just backed up ddEG4D6s to ./#ddEG4D6s.1#
And the calculation is not made (I wait more than ten minutes) and i obtain no ss.xpm
I dont understand what is the problem
This could easily be too short a time if there are multiple frames in
your pdb file. I don't know whether you have or need to follow the
suggestion I made last time...
http://www.gromacs.org/pipermail/gmx-users/2008-January/031720.html
Also, per "man do_dssp" you need to have set your DSSP environment
variable correctly.
Finally, test do_dssp on the same .pdb file you say works with dssp.
Mark
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