QUBEKit has been designed as a python command line toolkit with simple, intuitive commands allowing the user to perform three main tasks: 1) writing QM input files for atomsin-molecule, Hessian matrix and torsional scan calculations, 2) derivation of bond, angle, torsion and non-bonded MM parameters from the results of the QM calculations, and 3) the output of the parameters in widely-used MM topology and force field files. The only required inputs are the molecule's structure and some initial reference parameters, which are included in a BOSS z-matrix, which is freely available via the LigParGen web server (). LigParGen provides a straightforward interface for generation of z-matrices. Users can draw, enter the SMILES string or upload a PDB file of a molecule (up 200 atoms), which is then automatically converted to a z-matrix. The use of internal coordinates makes defining and choosing the dihedral angle to be optimized conceptually straightforward.