[gmx-users] dssp output of CG structure of 1K4C

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 18 19:03:45 CEST 2009

sunny mishra wrote:
> Dear all,
> I wanted to get the dssp output of Coarse Grained structure of my 
> protein i.e. 1K4C. In order to get that I have a script which is given 
> to me in the MARTINI tutorial (dssp2ssd.py). I have also downloaded the 
> dssp successfully in my linux machine. In my first step i cleaned the 
> 1K4C protein and renamed it as 1K4C_clean.pdb. 1K4C_clean.pdb consists 
> only the header title and atoms with C ligands in it. When i convert the 
> 1K4C_clean.pdb to CG structure using atom2CG script with the help of awk 
> command I get the CG structure successfully and I renamed it 
> 1K4C_cleancg.pdb. But when I am trying to get the dssp output of 
> 1K4C_cleancg.pdb using dssp it produces nothing but on the other hand it 
> produces the dssp output of my normal cleaned 1K4C pdb file. Do you know 
> if there is anyway I can get the dssp output of my CG structure of protein?

Not likely.  DSSP calculates secondary structure from hydrogen bonds, which will 
be absent in a CG model.  The script you refer to (dssp2ssd.py) does not use 
DSSP to calculate secondary structure; it simply converts DSSP output to the 
.ssd file needed by MARTINI.


> Thanks,
> Sunny
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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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