Abstract
Three systems of potential functions (PF) which are used in simulations of hydration of bioorganic molecules have been compared: Poltev and Malenkov (PM), Weiner and Kollman (WK) (used in the widespread AMBER program), and OPLS (optimized potentials for liquid simulations) of Jorgensen (J). The values of interaction energies of individual water molecules with single molecules of nucleic bases calculatedvia PM potentials are in somewhat better accord with mass spectrometric data than those calculatedvia WK PF. OPLS give much smaller energy values for all compounds considered; therefore they were not used in further computations. Monte Carlo simulation of hydration of 9-methyladenine, 1-methyluracil, and 1-methylthymine in systems with 300 water molecules and periodic boundary conditions have been performed. Simulations with PM potentials give better agreement with the experimental data on hydration energies than those with WK PF that allows to prefer PM PF for simulation of hydration of nucleic acids.
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