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 <jalem...@vt.edu
<mailto:jalem...@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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