Re-running DockOpt after dockfiles have already been generated results in new dockfile modifications every time due to randomness used in modifications (e.g. random perturbation of matching spheres). If any retrodock jobs are done, then they will not be re-run with the newly modified dockfiles, yet these newly modified dockfiles are what get copied to the best_retrodock_job/ directory at the end of the script. This results in a potential mismatch between the dockfiles that were docked against which proved to perform the best and the dockfiles that actually end up in the best_retrodock_job/ directory.
Re-running DockOpt after dockfiles have already been generated results in new dockfile modifications every time due to randomness used in modifications (e.g. random perturbation of matching spheres). If any retrodock jobs are done, then they will not be re-run with the newly modified dockfiles, yet these newly modified dockfiles are what get copied to the best_retrodock_job/ directory at the end of the script. This results in a potential mismatch between the dockfiles that were docked against which proved to perform the best and the dockfiles that actually end up in the best_retrodock_job/ directory.