ADL: Modelling water

Bhatia, Smita Smita.Bhatia at
Wed Sep 8 07:53:30 PDT 2004

Hi everyone,


The ligand binding site in my protein has 2 water molecules that could be
interacting with the ligand. How can I use autodock to model these waters? 


I also think that Autogrid will have to be changed so it would consider an
oxygen bound to 2 hydrogens as a potential bond acceptor, allowing for
correct treatment of water molecules. Can anyone suggest how to do this?


Thanks a lot,




Smita Bhatia

Institute for Biological Sciences

National research Council

100-Sussex Drive, Room # 3031

Ottawa, ON  K1A 0R6

Phone: (613)990-0855

Email : Smita.Bhatia at <mailto:Smita.Bhatia at> 



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