[gmx-users] do_dssp question

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 9 00:35:17 CEST 2009

Kirill Bessonov wrote:
> I have used do_dssp program to analyze secondary structure during 
> simulation of DMPC/DMPE. But I am not clear on installation of dssp.
> The program seems to work, I have set all the environmental variables so 
> that dssp binary is seen in /home/DSSP directory, but I am not sure if I 
> need to download the database of dssp files from the internet to make 
> this program work.

No libraries or other databases are necessary.

> There are 14 residues in your selected group
> Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time   52.000  
> Back Off! I just backed up ddoSxMLN to ./#ddoSxMLN.1#
> Last frame          0 time   52.000  
> 100%
> And I get ss.xps file that when I open it in image viewer is just a blue 
> line.

Then you've got a consistently helical protein.  It could be that your axes are 
skewed a bit, but you can change proportions using a .m2p file.  An example is 
available in the online manual.

> How should I properly setup the program and whether it will give me 
> %alpha helicity over the course of the trajectory, thank you

To calculate % helicity, make use of scount.xvg (the other default output).


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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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