This 32-page guidebook and this related 51-slide presentation discusses, with thorough illustrations, the computational chemistry research topic of docking of a drug-candidate ligand within a bio-macromolecule host target such as a receptor protein or an enzyme, using the free and simple AutoDock 4 and AutoDock Vina software (aided by ADT - AutoDockTools freeware as per its authoritative 2012 Tutorial by Ruth Huey et al, stored here also), followed by visualisation of the ligand-host interactions using the PyMOL and the Discovery Studio Visualizer, stressing on the ability to practically do such docking computations and visualisations.

This presently growing guidebook (at present 11 pages) is discussing, with thorough illustrations, the computational chemistry research topic of molecular dynamics simulation, employing the simple Tinker freeware at present (to be followed later with more detailed Gromacs and Amber22 freeware) and the associated MD visualisation (e.g., this one) using the VMD freeware, along with solvation by Packmol - but at first starting with the much needed corrections of the downloaded PDB structures using Chimera, MODELLER and Swiss PDB Viewer freeware. The booklet stresses on the ability to practically do such MD simulations along with the RMSD variation analysis and the image/video visualisations.