VMD-L Mailing List

From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Fri Jun 05 2009 - 10:14:11 CDT

hello everyone...
i have two pdb files: protein(has four chains) and a lignad,,
the protein and the ligand both have a cysteine molecule . i.e the
interaction include the disulphide link between Cys(93 in B chain) and cys
of ligand.
i.e i want to add a covelent bond(disulphide bridge) between the cys of
protein and cys of ligand.

The approcah that i followed include:
i loaded both the molecules and align the sulphur atoms as much as possible
spatilally.
in the mouse menu, i clicked on the add/remove bond option and selected the
sulphur atoms.but that doesn't seem to work beacuse,that works only for
atoms in the same molecule...

After obtaining the disulphide bond, i want the a pdb file of this
complex.(protein and ligand connected by cysteine residues).
The structure of the protein-ligand complex is not available in the PDB.

can anybody help me in this regrad? 

-- 
Gurunath M Katagi
M.Sc (engg) Research student
Supercomputer Education and Research Centre
Indian Institute Of Science
Bangalore