[Dock-fans] Amber score "divide & conquer"

[Francesco Pietra]

I am sampling a big protein for small_molecule docking by creating
selected_spheres/boxes for parts of the protein. Grid for the whole
protein would be too big. Also,e creating models for parts is
difficult because each chain lengthens along the whole protein.

Suppose that the same small molecule docks in more than a single part
of the multimer, could amber re-score for docking on a part be
directly compared (energy by energy) with amber re-scoring for another
part?

Thanks
francesco pietra