We report on a hybrid scheme to perform efficient and accurate simulations of scanning tunneling spectroscopy (STS) of molecules weakly bonded to surfaces. Calculations are based on a tight binding (TB) technique, including a self-consistent calculation of the electronic structure of the molecule, to predict STS conductance spectra. The use of a local basis makes our model easily applicable to systems with several hundreds of atoms. We performed first-principles density-functional calculations to extract the geometrical and electronic properties of the system. In this way, we can include, in the TB scheme, the effects of structural relaxation upon adsorption on the electronic structure of the molecule. This approach is applied to the study of regioregular poly(3-dodecylthiophene) polymer chains adsorbed on highly oriented pyrolytic graphite. Results of spectroscopic calculations are discussed and compared with recently obtained experimental data.