What are all of the different ways to derive the partial charges, van der Waals interactions, bond lengths, etc. of an amino acid (in other words, all of the parameters that could be used in a molecular mechanics force field or other related method - such as a Poisson-Boltzmann equation solver)? I'm especially interested in the strengths and weaknesses of each method.

Complete fitting protocols would be greatly appreciated, although all I'm really looking for is a few sentences describing each method and its broad strengths and weaknesses.