Description

This tool calculates a confounding box around an input ligand or pocket and uses it to generate the input parameters for an AutoDock Vina job.

If you already know the coordinates of a ligand which binds to the protein, you can simply use this file as the tool input. Alternatively, you can search for pockets using the fpocket tool and use one of the output PDB files as an input.

The output file can be fed into the AutoDock Vina tool as an alternative to creating the parameter file manually.

Inputs:

This tool requires:

• An input file (MOL, SDF, PDB or MOL2 format) representing either a ligand, or a pocket found with the fpocket tool.
• (OPTIONAL) Buffers for each direction (x,y,z), which defaults to 0 Å. This value will be added to the confounding box that the tool generates in each respective direction. We recommend that you visualise the calculated box from an initial run of this tool, and calculate the expansion needed in each direction to cover the area of the binding site you wish to explore.

Output:

The output for this tool is a txt file containing the parameters needed to run an autodock vina docking calculation with the docking tool. For example:

size_x =  12.443000000000001
size_y =  11.888
size_z =  9.290999999999997
center_x =  -29.8395
center_y =  4.364
center_z =  -64.5925
num_modes = 9999
energy_range = 9999
exhaustiveness = 10
cpu = 4
seed = 1

The values for num_modes, energy range, cpu and seed are set to default values here.

This file can be used as the box parameter for the docking tool.