Molecular dynamics simulations on the wild-type AmtB protein and its D160A homology model have been performed. Although no significant structural changes due to the mutation of Asp 160 were observed, calculations confirmed the critical role of Asp160 for the recognition and binding of NH4+ in AmtB. The carboxyl group of Asp 160 is similar to 8 angstrom from NH4+, but their favorable through-space electrostatic interaction is further enhanced by a hydrogen bond chain involving Ala 162 (the backbone carbonyl group) and Gly163 (the backbone amide group). This explains the occurrence of the second binding site in AmtB which does not exist in the D160A mutant, as shown in the computed energy profiles. As the initially buried carboxyl group of Asp160 links to the ammonium ion in the periplasmic binding vestibule through a chain of water molecules, a likely deprotonation venue thus is from ammonium to Asp160. Combined QM(PM3)/MM molecular dynamics simulations showed that indeed Asp160 can serve as the proton acceptor and the overall proton transfer process needs to overcome a barrier of merely 7.7 kcal/mol, which is in good agreement with our previous QM(DFT)/MM optimizations. Significantly, the proton transfer adopts an unconventional mechanism by migrating the negative charge from the carboxyl group of Asp160 to NH4+ via two water molecules, which can be illustrated as -CO2-center dot center dot center dot H2O center dot center dot center dot H2O center dot center dot center dot NH4+ --> -COOH center dot center dot center dot H2O center dot center dot center dot OH-center dot center dot center dot NH4+ --> -COOH center dot center dot center dot H2O center dot center dot center dot H2O center dot center dot center dot NH3. Apparently, this is also a charge recombination process and thus is exothermic.