The structure of the system in QM/MM calculations is provided by the restart file (extension .rst) and not by the geometry block as it would be for pure QM calculations. The parameters of classical interaction are given by the topology file (extension .top). These two files are REQUIRED for QM/MM calculations and can be generated by the prepare module. In a typical setting this “preparation stage” is performed separately from the main QM/MM simulation.

  - [Prerequisites](QMMM_Preparation_Prerequisites.md)
  - [QM region definition](Qmmm_preparation_basic.md)
  - [Solvation](Qmmm_preparation_solvation.md)
  - [Permanent Constraints](Qmmm_preparation_constraints.md)