Search box size and coordinates

[RMeli]

The values for the search box size and coordinates are given in the section "Prepare the protein using AutoDockTools".

Since we did not use AutoDockTool this year, it could be beneficial to report such values on the section "Prepare a docking configuration file" as well.

[IAlibay]

Bring this from the team discussion: one proposed alternative here is to skip all this and use the binding pose of another bound ligand as an input for the grid center.