We recently incorporated parameters to simulate
Ca2+ ions in a fully unbiased fashion. vdW parameters are set in such a way
that a large radius is used to interact with solvent, while Calcium-protein
contacts are calculated with a smaller size. This allows negative moieties to
coordinate Ca2+ mostly because of electrostatic stabilization and without
imposing specific constraints. Use of these parameters in a Calmodulin system
helped to rationalize the effect of an Ataxia-related point mutation in PMCA3
(click here to see the publication).