ADL: Considering water molecules in vina docking

Oleg Trott trott at
Fri Feb 21 12:27:20 PST 2014


On Fri, Feb 21, 2014 at 6:16 AM, meginir urestal
<meginir.urestal at> wrote:
> Hi,
> I was wondering how to go about considering a crystallographic water
> molecule in vina docking.

The canonical way to do this would be to remove the waters -- that's
how the scoring function was trained and tested.

However, if you have reasons to believe that keeping the waters is
better in your case, you can do that.

> Do you simply keep the oxygen?

You'd probably want to add the hydrogens, because otherwise the waters
will just be H-acceptors, not H-donors.

>  Do you add the hydrogens (but then there's the fact that the
> prepare_receptor script doesn't merge water molecule hydrogens).

They shouldn't be merged, since they are polar hydrogens.

>  Do you keep the HETATM or do you change it to ATOM?

This shouldn't matter to Vina.


Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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