The relevance of the fragment relaxation energy term and the effect of the basis set superposition error on the geometry of the BF3... NH3 and C2H4... SO2 van der Waals dimers have been analyzed. Second-order Moller-Plesset perturbation theory calculations with the d95(d,p) basis set have been used to calculate the counterpoise-corrected barrier height for the internal rotations. These barriers have been obtained by relocating the stationary points on the counterpoise-corrected potential energy surface of the processes involved. The fragment relaxation energy can have a large influence on both the intermolecular parameters and barrier height. The counterpoise correction has proved to be important for these systems.