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

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


Chrystal,

If you are asking about multiligand docking, the support for it has
been removed back in 2008, primarily due to little interest among the
users: http://mgldev.scripps.edu/pipermail/autodock/2008-August/004377.html

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
following:

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.

Oleg

On Thu, Oct 11, 2012 at 7:20 AM, Chrystal Bruce
<chrystal.d.bruce at gmail.com> 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
> ________________________________________________
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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