ADL: Considering water molecules in vina docking

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


Hi

On Fri, Feb 21, 2014 at 6:16 AM, meginir urestal
<meginir.urestal at gmail.com> 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.

HTH

-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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