Regarding the Lennard-Jones terms, Amber99SB-disp alters the parameters of aspartate, glutamate, and arginine, leaving open the possibility of more accurate interactions between lysine and other charged residues in the protein as the source of the discrepancy; however, more notable was the inclusion of the Best et al. lysine partial charges (i.e., Amber99SB*-ILDN-Q ) with Amber99SB-disp. Although both Amber14SB and Amber99SB*-ILDN have the same partial charge assignment, Amber99SBdisp uses altered backbone charges for aspartate, glutamate, lysine, arginine, and protonated histidine (Figure ). These were developed to correct for aberrant helical propensities and create consistency between the amino acids; all but these five residues have the same assigned backbone partial charges.