ADL: Modelling water

Bhatia, Smita Smita.Bhatia at nrc-cnrc.gc.ca
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

 

**************************************

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 nrc-cnrc.gc.ca <mailto:Smita.Bhatia at nrc-cnrc.gc.ca> 

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