In this work a computational approach to investigation of template/monomer complex in imprinted polymers, enable us to select monomers interacting strongly with the melamine, as target analyte. The molecular modeling and performing thermodynamic computations were carried out with the help of a patented protocol developed at Cranfield University, UK. The binding energies shows the acrylamido-2-methyl-1-propanesulfonic acid (AMPSA) is the best binding monomer for melamine followed by itaconic acid and F22 ethylene glycol methacrylate phosphate (EGMP).