The therapeutic agents mostly act by interacting with a biological macro-molecule, say by activation of a receptor or inhibition of an enzyme or inter-calating into the DNA etc. These interactions can be understood by examining the 3D structures of the drug. The structural analysis of the drug-receptor complex can be appreciated if the macro-molecule is seen in pure crystalline form, but such crystallisation of most receptors is difficult. It is in this context that models of the receptors and their complexes with ligand are constructed by molecular modelling. It is a computer-based method. In its simplest form, it involves converting each atomic coordinate into a corresponding screen coordinate and then connecting the appropriate atoms by lines representing bonds. Most molecular modelling studies start with the selection of a model that describes the intra- and inter-molecular interactions in the system. The two most common models that are used are quantum mechanical and molecular mechanics. Molecular mechanics treat each atom as a ball of mass proportional to its atomic weight. Each bond is treated as an analog of a mechanical spring. The total potential energy of the molecule is computed by assessing the bond stretching, angle bending and torsional motions. In quantum mechanical approach, the quantized wave-like behaviour of the electrons and the nuclei is assessed.