ADL: about vina input

Mark Swingle mswingle at jaguar1.usouthal.edu
Thu Apr 16 10:54:42 PDT 2009


On Thursday 16 April 2009 11:43:06 am Gonçalo C. Justino wrote:
> Dear all,
>
> I've been playing around with Vina and I'm quite fascinated by its
> behaviour so far. There is just this basic question that keeps coming back.
> While defining the input, I'm been using
>
> --center_x 0 --center_y 0 --center_z 0 --size_x 120 --size_y 120 --size_z
> 120
>
> and my question is: this corresponds to a "box" centered at (0,0,0) with a
> "box" of 120 or with a "box side" of 60 ? Or is this the wrongest possible
> interpretation?
>
> Any comments are welocme,
>
> Gonçalo

That would be a box with its center at (0,0,0) and 120 Angstroms along each 
edge/side. In other words, HUGE :-) To translate an autodock box to a vina 
box, use the gridcenter triplet from your gpf file for center_x center_y 
center_z, then multiply the npts triplet by the grid spacing to get size_x 
size_y size_z. For example:


npts 88 48 66                        # num.grid points in xyz
spacing 0.375                        # spacing(A)
gridcenter 13.206 19.14 30.8         # xyz-coordinates or auto

becomes............

--center_x 13.206  --center_y 19.14  --center_z 30.8

--size_x 33   --size_y 18   --size_z 24.75

Regards,

Mark



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