We have investigated photoabsorption spectra of bovine rhodopsin and its Mutants (E122Q and E113Q) by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations as well as retinal in vacuo by pure QM calculations, employing, multireference (MR) ab initio and TD-B3LYP methods. The sophisticated MR-SORCI+Q and MRCISD+Q methods extrapolated with respect to adopted approximations can reproduce the experimental absorption maxima of retinal very well. The relatively inexpensive MR-DDCI2+Q method gives absorption maxima blue-shifted by ca. 65 nm from experimental values; however, this error is systematic and thus MR-DDCI2+Q can be used to estimate spectral shifts. In MR calculations, the ground-state energy of retinal at B3LYP geometry is significantly lower than that at CASSCF geometry. Therefore, B3LYP geometry is more reliable than CASSCF geometry, which has a blue-shift error as large as 100 nm in the gas phase. The effect of ground-state geometry on the excitation energies is less critical in the polarizing field of protein environments. At the B3LYP geometry, there is no significant charge transfer,upon vertical excitation to the S-1 excited-state either from Glu113 to retinal or from Schiff-base terminal to beta-ionone ring through the polyene chain. All-trans to 11-cis isomerization of retinal in the gas phase has no influence on the calculated S, absorbing state, in agreement with experiment. The shoulder of the experimental absorption spectrum of retinal in vacuo at the S-1 absorbing band appears to be the second electronic transition (S-2) in our calculations, contrary to previous tentative assignment to vibrational state of S-1 or to the S-1 band of a retinal isomer.