The protein three-dimensional crystal structure of Human Epidermal Growth Factor Receptor 2 (PDB ID 1N8Z) is obtained from Protein Data bank and is prepared for the analysis, using protein preparation wizard. In the protein preparation step, protein minimization, grid generation and docking of ligands were done using Glide Schrodinger package . The Hydrogen atoms were added to the protein for maintaining the ionization and tautomeric state of Asp, Glu, Ser, His and Arg amino acids. The missing side chains and atoms are corrected, followed by the protein structure minimization using force fields to minimize the steric clashes in the structure. This protein structure was used for the grid generation in further docking analysis.