While minimizations of several discrete structures using through-space forces may look correct, please understand the theory behind the force field you are using and that any force field not specifically developed or parameterized for intermolecular forces will not lead to experimentally accurate coordinates. The RCSB PDB also provides a variety of tools and. Please note, while you are able to optimize the entire scene, most force fields are not parameterized for multiple discrete molecular structures, and you will be relying on the through-space forces defined in the force field (mainly van der Waals and electrostatic), if defined at all. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. To do this, you can change the optimization scope to optimize the entire scene. However, you may wish to optimize several discrete molecular structures at the same time and in relation to each other. ChemDoodle 3D therefore will optimize molecular structures separately and individually as you are editing them. Most small molecule force fields are optimized for describing individual discrete molecular structures.
