Before starting the docking calculations, ensure that the docking software is properly installed on your system. You may also need additional software for preparing the inputs and analyzing the results. The setup of docking calculations involves several critical steps to ensure accurate and efficient simulation of ligand-receptor interactions. In general, each software has a proper set of parameters. One step involves defining the search space within the protein, usually by setting up a grid around the binding site. This can be based on known ligand binding data or predicted using software tools that identify potential binding pockets. The binding site can be defined using coordinates or by selecting specific residues. Parameters such as grid size and spacing are crucial because they influence the accuracy and speed of the docking process. Some programs allow you to adjust the scaling of van der Waals radii and specify the ligand size to be docked and to define constraints to bias the docking if the docked poses do not match experimentally validated poses.