The complete modelling of passive scattering proton therapy systems is challenging and requires simulation tools that have capabilities in both beam transport and in the detailed description of particle-matter interactions. Beam Delivery Simulation (BDSIM) allows the seamless simulation of the transport of particles in a beamline and its surrounding environment. A complete 3D model can be built from Geant4, CLHEP and ROOT to provide a complete analysis of the primary beam tracking. This capability is applied to the eye treatment proton therapy machine part of the IBA Proteus Plus product line. Those simulations are compared with a fast in-house particle tracking code with a semi-analytical model of Multiple Coulomb Scattering. The preliminary results leading to the detailed knowledge of the beamline performance are discussed in detail.