ADL: Grid co-ordinates!!!

raghu bhagavat rag_vocal at yahoo.co.in
Sun Apr 5 23:20:14 PDT 2009


Thanks for the reply........
yes i know the option of giving the entire macromolecule as the grid box..........but this can be done in ADT or any GUI ........but how to give the option of grid co-ordinates if u dont knw the point in Autodock-Vina.......this is my question.........In the configuration file, we specify the co-ords where the grid has to be built.......Now, we dont know the co-ords.......so what next......how to specify the grid box in "Autodock4-Vina".........not in other versions of AD........

--- On Sat, 4/4/09, bagdevi.mishra at gmail.com <bagdevi.mishra at gmail.com> wrote:

From: bagdevi.mishra at gmail.com <bagdevi.mishra at gmail.com>
Subject: Re: ADL: Grid co-ordinates!!!
To: autodock at scripps.edu
Date: Saturday, 4 April, 2009, 3:54 PM

grid provides the search space for the ligand, if you do not know where in
the receptor the ligand binds, you can provide a grid that covers the whole
receptor. it would be time consuming, but it would solve your purpose.

Regards,
Bagdevi Mishra.



On Wed, Apr 1, 2009 at 7:08 PM, 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..........
>
> So for mass operations (Virt. Screening), how to proceed for this problem??
>
> Kindly suggest
>
>
>
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