ADL: Grid co-ordinates!!!

Oleg Trott trott at scripps.edu
Mon Apr 6 16:21:15 PDT 2009


Raghu,

On Wed, Apr 1, 2009 at 6:38 AM, raghu bhagavat <rag_vocal at yahoo.co.in> wrote:
> Hello all........
> I have a query in AD Vina version........
> the configuration file has to be given with x, y, z coordinates for building the grid...What if we dont know where the ligand has to bind.....This will arise in while doing Virtual screening......
> When we use Autodock4 version on command line, the "auto" option is done if the grid-centre is not specified and it runs taking the option "auto"..........But unlikely in Vina version..........
>

"auto" does not make autogrid guess the binding site. It simply
centers the grid maps on the center of mass.

> So for mass operations (Virt. Screening), how to proceed for this problem??

Normally, virtual screening is done with one or several very related
receptor structures and many ligands. The user typically would either
know the location of the binding site or target a particular spot in
the receptor.

If this is not the case for you, you can either use a program that
guesses the binding site location (e.g. AutoLigand is included with
MGLTools), or make the search space big enough that it includes the
whole receptor with some margins (in which case, you will probably
want to increase "exhaustiveness")

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

http://olegtrott.com


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