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

[Justin A. Lemkul]

sunny mishra wrote:
> Hi Justin,
> 
> Thanks for the expedient reply. So in that case I cannot get the dssp 
> output of my CG structure for sure. So in that case do I have to get the 
> .ssd files of my 1K4C_clean.pdb file only right and then get the .seq 
> file of 1K4c_clean.pdb in order to proceed. Am I right?
> 

Right, to generate the MARTINI topology you need both .ssd and .seq files.

-Justin

> Sunny
> 
> On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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.
> 
>     -Justin
> 
>         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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================