ADL: Using Vina to dock 2 small molecule ligands into the minor groove of DNA

Oleg Trott trott at
Fri Oct 12 14:26:23 PDT 2012


If you are asking about multiligand docking, the support for it has
been removed back in 2008, primarily due to little interest among the

The following is tedious, and probably not the best approach, but the
only way to do "multiligand docking" with Vina now is to do the

1. Dock the first ligand (let's assume it returns 10 binding modes).

2. Make each of the binding modes part of the receptor, in turn; and
dock the second ligand to each of the results (let's assume you get 10
binding modes).

You will then have 100 2-ligand poses  that you could try to rank.

I may have heard of a script/wrapper that goes through the above steps
automatically, but I'm not sure.


On Thu, Oct 11, 2012 at 7:20 AM, Chrystal Bruce
<chrystal.d.bruce at> wrote:
> I am trying to dock two small molecules into the minor groove of DNA
> and have been having difficulties.
> As much as I would like sequential docking to work, the first molecule
> occupies more of the docking site than I would like, so I am trying
> simultaneous docking.
> I was able to write a .pdbqt that should have have both ligands, but
> my problem is that Vina is only reading the first molecule in the
> .pdbqt and docking that.  It is as if there isn't a second molecule
> there.
> Does anyone know if this is something about how Vina reads the pdbqt
> file or if there is something else I can do to convince Vina to try to
> dock both molecules?
> I searched the archive, but couldn't find an answer to this.
> Thanks,
> Chrystal
> ________________________________________________
> --- ADL: AutoDock List  --- ---

Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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