In the preceding paper (DOI 10.1021/jp902428x), we have derived the polarized force field "PBR" for bacteriorhodopsin (BR) using hybrid methods which combine density functional theory (DFT) with molecular mechanics (MM) models. This polarized force field has enabled extended molecular dynamics (MD) simulations of BR's chromophore binding pocket which closely preserve the experimentally well-known structure. Here, we employ the PBR-MD trajectories obtained for the conformational substates prevalent at physiological temperatures as material for the DFT/MM computation of the chromophore's vibrational spectra. By comparison with DFT results on the structure and vibrational spectra of an isolated chromophore, we identify the structural and spectral changes induced by the protein environment. Comparisons with the wealth of experimental data available in the literature on the chromophore's vibrational spectra yield estimates on the accuracy of the DFT/MM descriptions. We discuss why highly accurate DFT/MM. descriptions are expected to become a decisive tool for solving the long-standing enigma of how the light-driven proton pump BR actually works.