[gmx-users] dssp programm

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 20 15:29:47 CEST 2009

subarna thakur wrote:
> Hello
> I installed the dssp program for obtaining the secondary structure.I 
> used the dssp programm to analyze the secondary structure of the protein 
> after a MD simulation run. I got the out of the pogramm as m.dssp but I 
> want to know how do I represent the output of the dssp programm 
> graphically or how do I visualize the output of the dssp programm.

If you are using dssp as a standalone executable, you'll just get a text file 
with some statistics.  If you want the nice pictures you see in publications, 
you have to use do_dssp, which acts as an interface to dssp, and can be used 
with trajectories.


> regards
> subarna
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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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