Calculating free energy differences is a topic of substantial interest and has many applications including chemical reactions which are used in organic chemistry, biochemistry and medicines. In equilibrium free energy methods that are used in molecular simulations, one molecule is transformed into another to calculate the energy difference. However, when the compared molecules have different number of atoms, these methods cannot be directly applied since the corresponding transformation involves breaking covalent bonds which will cause a phase transition and impractical sampling. Thus, Quantum Mechanical Simulations, which are significantly more demanding computationally, are usually combined to calculate free energies of chemical reactions. Here we show that the free energies can be calculated by simple classical molecular simulations followed by analytic or numerical calculations. In this method each molecule is transformed into its replica with the VDW and Coulomb terms of the different atoms relaxed in order to eliminate the partition function difference arising from these terms. Then, since each transformed system can be treated as non interacting systems, the remaining difference in the (originally highly complex) partition function can be directly calculated. Since molecular force fields can often be automatically generated and the calculations suggested here are rather simple the method can form a basis for automated free energy computation of chemical reactions.