[gmx-users] do_dssp file format

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jan 14 12:26:17 CET 2008

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... 

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.


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