Question

Why waters molecules were removed in protein preparation?

Answer 1

In most cases, water molecules are not involved in the binding. They are therefore deleted to make computations easier and clear the binding pocket of possible water molecules that would distort the pose search. Remember that in docking you typically search for molecules that can create multiple favorable contacts to the protein, water molecules might confound this procedure.

That said, if it is known that one or more water molecules are involved in the binding of molecules to the target and its activity, those water molecules should be preserved. So it depends on the target, and you should read on the currently accepted binding mechanism before starting your docking calculations.