In order to analyze molecular vibrations, a method based on the calculation of the Fourier frequency spectrum of supercomputer amplitude-time realizations of the integral dipole moment in supercomputer simulation of glycine, Diphenyl-L-alanine, and tryptophan has been implemented. Under conditions of a zero external electromagnetic field, the frequency spectra of natural local vibrations of the atomic subsystem of the molecule were established to be the results of spectral analysis of these realizations. The spectra were verified by comparison with the known literature data on quantum chemical computing, computer simulation and experimental spectroscopy. It was shown that the proposed complex and technique made it possible to efficiently calculate reliable spectra of local amino acid vibrations. The results obtained may be useful for the development of prototypes of hybrid semiconductor microelectronic devices with built-in biomolecular components.