AmtB from Escherichia coli is a transmembrane protein with an important role in ammonium transport, especially at low external ammonium concentrations. However, whether AmtB is a channel that permeates NH3 or an NH3/H+ co-transporter is still an open question. An extensive series of hybrid Quantum Mechanical(QM)/Molecular Mechanical(MM) simulations has been performed to investigate the mechanism of ammonium transport through AmtB. Focus has been placed on the deprotonation of ammonium and the possible co-transport of H+ and NH3. Constraint dynamics simulations have been used to obtain the potentials of mean force for the possible NH4+ deprotonation paths involving water molecules and/or protein side chains. Further investigations on the transport pathways of H+ and NH3 have shown the details of the co-transport mechanism. The distribution of solvent and ammonia inside the pore is also analyzed and the possible mechanisms of ammonia re-protonation and how side chains are reset back to original state are presented.