In the present work a mathematical model has been presented to study the behaviour of five-zone simulating moving bed (SMB) system for the separation of a ternary mixture of certain amino acids. These are methionine, phenylalanine and tryptophan, possessing linear isotherms values. Safety margin method has been used to design the SMB system while triangle theory became the basis to calculate the operating conditions at fixed feed flow rate. It was found that for same safety factor (beta) value in each zone, increase in beta value causes the purity values of all product streams to increase up to a definite value. Further increase in. value shows the effect of decrease in separation efficiency, because of dominance of axial dispersion and mass transfer resistances. The effect of zone safety factor (zone flow rate beta(II), beta(III) and beta(IV)) values on the separation performance of five-zone SMB have also been investigated which remained an important issue in SMB current research. Increase in beta(II) value results in rising tryptophan purity, phenylalanine purity improves due to increase in beta(III) value and increase in beta(IV) value becomes the basis for enhancing methionine purity. In column profile study, the solute concentration profile diminishes due to increase in particular separation zone safety factor value. This happened due to low column switching time with high desorbent flow rate to the system. The developed mode was run in Aspen Chromatography vis 12.1. (2004) simulator for simulation studies.