ADL: Including water molecules in docking

Gavin Seddon home at
Thu Apr 2 05:45:21 PDT 2009

Douglas Houston wrote:
> Hi all,
> I've noticed that in one of my structures there's a very stable-looking water molecule that might well allow for water-mediated hydrogen bonding when ligands bind. I also notice all water molecules get removed when converting the receptor pdb to pdbq. Is there any way to get Autodock to use this water molecule, for example perhaps by treating it as part of the binding site?
> thanks for any input,
> Doug
the python script
uses a '-U' ARGUMENT that removes water, use scrpts, without -U and do 
other cleanup with alternate software; or prep molecule another way.
This is a really interesting point.

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