ADL: grid box help

Devl Devel devl.development at gmail.com
Wed Dec 17 14:05:49 PST 2014


Hi Keti

I'm not sure if this helps, but I have a tool that helps generate bounding
boxes based in amino acid positions in Angstroms.

https://github.com/devldevelopment/dockingbox

Normally I define boxes around amino acids of interest and add extra space
to the bounding box to allow ligand flexibility. Vina is a
stochastic/statistical method so it's likely that even with the same box
you will get different affinities. By no means am I an expert these are
just my thoughts and experiences. Please let me know if you want help with
the tool or what your particular use case is.

Cheers
Dev



On Wed, Dec 17, 2014 at 8:35 PM, Keti Bardhi <keti.bardhi at hotmail.com>
wrote:
>
> Hello, I am new to Autodock Vina and I am having a problem in defining
> the grid box coordinates.  Does the binding affinity change in base of the
> grid box coordinates. How precise should they be ? I have tried different
> ways to calculate the grid box and I get different binding affinities.
>
> Thank you.
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