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

sunny mishra mishra.sunny at gmail.com
Tue Aug 18 18:57:46 CEST 2009

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?


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