ADL: Considering water molecules in vina docking

meginir urestal meginir.urestal at gmail.com
Fri Feb 21 06:16:27 PST 2014


Hi,

I was wondering how to go about considering a crystallographic water
molecule in vina docking. Do you simply keep the oxygen?
 Do you add the hydrogens (but then there's the fact that the
prepare_receptor script doesn't merge water molecule hydrogens).
 Do you keep the HETATM or do you change it to ATOM?

Meginir,


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