Noncovalent interactions, such as van der Waals interactions, hydrogen bonds, salt bridge and cation-pi interactions play extremely important roles in biological systems and, in contrast to covalent bonds, many such noncovalent interactions are not well understood. In the present work a new protocol has been developed to measure the enhancement of binding energies due to cation-pi interactions between aromatic amino acids and organic or metal ions. Investigation of the cation-pi interactions will provide further insight into the structure and function of biological molecules.