We include additional scripts and programs (called the API) for preparation, running, and analysis of the simulations. For preparation of the SEEKR2 calculation, we include a utility that *6 prepares the file tree and files for a SEEKR2 calculation, typically using concentric spherical milestones defined by the distance between the center-of-mass (COM) of atoms of a receptor binding site and the COM of a ligand molecule used in our first MMVT SEEKR paper. For the convenient control of the SEEKR2 calculation, we include software that can be called with a single line that can run the simulations for any or all of the anchors and simulation regions.