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

[sunny mishra]

OK. Thanks a lot justin

On Tue, Aug 18, 2009 at 1:16 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
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