The Molecular Graphics Laboratory Forum

Good afternoon!

I'm using the AutoDock Vina, to do some dockings, but I have a problem, my ligands are out of the box after make dockings? I try many times but always, the ligand go outside.


Best Regards.
Freddy Rodrigues

ciao

pay attention to the grid spacing!

in the pic u sent it is 0.5.
it should be 1, because vina expects the size of the box to be expresed in A, while ADT generates boxes whose size is in grid points.

enjoy

mind the grid spacing Fred!

you've set it to 0.5. that means the box is 2x2x2 time larger than u think. that's why the lingandr are placed "outside"

Hi PESA!!

Thank you for the reply. My question is, how I put in the conf.txt file the spacing is 1? Like below or automatically the Vina program assume the spacing is iqual 1.

receptor = protein.pdbqt
center_x = -2.745
center_y = 8.689
center_z = 53.707
size_x = 30
size_y = 30
size_z = 30
exhaustiveness = 100
num_modes = 1
spacing = 1

Freddy