Introduction: In chemical biology and biomolecular engineering, rational design is the strategy of creating new molecules with certain functionality, basedupon the ability to predicthowthe molecule\\\\\\\\\\\\\\\'s structure will affect its behavior through physicalmodels. The use of rational design techniques for proteins is a major aspect of protein engineering. Materials and Methods: All simulations were carried out using gromacs 4.5.3 package and gromos96 force field. Also, docking simulations performed using autodock vina software package. Results: O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydratemoiety. In thiswork, three different structures o alphaamylasewere prepared theoretically in such a way that totally 150 residues of protein abstracted from Cterminal. Then three differentmoleculardynamics simulationwas ran to compare active site of engineered proteins. The RMSD values of residue making sitewere evaluated to study the active site changes. Similarly 30 different size structures were prepared via remove the C-terminal residues of enzyme. In each structure five residues was abstracted; by using the docking simulation scheme affinity of binding of enzyme to malto triose evaluated by using the calculation of free energy of binding. Conclusion: The obtained results were shown the regular change in active site affinity of binding

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