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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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