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

[sunny mishra]

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?

Sunny

On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul <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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>>
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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
>
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