In most current molecular mechanical program packages polarizability and charge transfer effects are not taken into account. Socalled charge equilibration (or fluctuating charge) methods allows for these effects: In stead of having fixed point charges at the positions of the nuclei, these charges change in respons to the external electric field (from the surroundings). A simple real example of such effects is the difference of dipole moment for the water molecul between gas phase (1.85 D) and solution (about 2.6 D). This is caused by the influence of the surrounding water molecules in solution.
Locally we are particularly interested in metal ions in biological systems, and both polarizability and charge transfer are expected to be very important in metal ion complexes.
The idea of charge equilibration is based in density functional theory (electronegativity equilization). The simplest model [Rappé and Goddard III, 1991] [Rick et al., 1994] maintains the concept of point charges, but let them vary. How they vary depends on the local electric field and on properties of the given atom (ionization potential, electron affinity and atomic radius). In more advanced methods [York and Yang, 1996] [Itskowitz and Berkowitz, 1997] an actual charge density is introduced - a step towards density functional theory.