The origin of the interactions occurring in the calmodulin protein interacting with one of its target peptide and counterions, and binding four calcium dications, has been investigated in the gas phase, using the many-body model presented in Paper I [Masella and Cuniasse, J. Chem. Phys. 119, 1866 (2003)] and a classical pairwise force field. As compared to the latter force field, the many-body model is shown to provide a geometrical description of the calmodulin/target peptide structure in better agreement with the x-ray experimental one, and a better description of the Ca2+ binding sites (as compared to "small molecule" structures reported in the Cambridge Structural Database). Regarding the energy, both models provide qualitatively a similar description of the interactions occurring in the calmodulin/target peptide system. However, quantitatively, the pairwise model predicts interaction energies greater by about 25% as compared to the many-body one in the case of calmodulin/Ca2+ interactions. This is due to the inability of pairwise force fields to account for the strong anticooperative effects predicted to occur in [Ca,(carboxylate)(n)](2-n) systems by both the many-body model and quantum computations. Hence, the new many-body model appears to be well suited for describing proteinic systems interacting with cations, both in terms of geometry and energy. (C) 2003 American Institute of Physics.