We present a numerical simulation of the HCl acidification process of a three-dimensional semiconducting emeraldine base (EB) polymer leading to the corresponding metallic emeraldine salt form. We have searched minimum energy paths connecting the initial configuration, composed of two EB polymer chains per cell each one attached by two HCl molecules, with the Pc2a polaronic configuration which is the final state of the acidification process. For this aim, the variational nudged elastic band method has been adopted. We provide a pictorial representation of the acidification process at T=0 K, monitoring the EB protonation and the evolution of the polymeric chains and of the positions of the Cl(-) counterions on the lowest potential energy surface. To include also temperature effects, we have explored the potential energy surface around the final equilibrium configuration, heating the system and following its dynamics by the Car-Parrinello procedure.