Q: In AutodockTools protocols, we acquire to add some charges to the calculation sample whether it is Kollman charges or Gasteiger charges. What is the difference between them, and how to select the best to our sample?
Answer:
The main difference is that the Kollman charges are template values for each amino acid that were derived from the corresponding electrostatic potential using quantum mechanics, whereas the Gasteiger(-Marsili) charges are determined on basis of electronegativity equilibration, which can be computed by AutoDockTools for the given molecular system i.e. your ligand or co-factors in case you don't have any partial charges at hand.
You may of course also use Gasteiger charges for the protein, since both approaches yield similar atomic charges. The only problem is that the Gasteiger method assumes an overall net neutral state for the respective molecular system. Thus, check the protonation states of the amino acids and the ligand. I had good success using Kollman charges for the protein and Gasteiger charges for the ligand and cofactors. In case where the ligand is charged either use quantum chemically derived atomic charges or modify the obtrained Gasteiger charges manually (e.g. more negative values on carboxylate oxygens).
Source:
What is the differences between Kollman and Gasteiger charges? - ResearchGate. Available from: https://www.researchgate.net/post/What_is_the_differences_between_Kollman_and_Gasteiger_charges [accessed Aug 12, 2016].
