MMMx uses third-party software for tasks where well-tested solutions are already available in the form of executables.
SCWRL4 is used for adding or modifying amino acid sidechains in module Flex for loop modeling, in module Prepare for mutations, sidechain repair, and sidechain repacking, and in module YasaraRefine for optional repacking before calling YASARA in order to repair serious clashes that may upset YASARA. Download from the Dunbrack lab requires a license application for non-profit users.
If DSSP is present, MMMx can perform DSSP analysis upon loading PDB files. In version 1.0, this is of interest only for programmatic access. None of the current modules relies on DSSP secondary structure information.
YASARA structure is the core of module YasaraRefine. YASARA structure requires a paid license. In some cases, it is advisable to perform such refinement on the raw ensemble before using module EnsembleFit. As an alternative, the raw ensemble, which is a set of PDB files can be refined with external software. In many cases it is sufficient to refine the fitted ensemble.