As @jherbert said, using the interfaces between Q-Chem and other MM packages is the most straightforward way to do QM/MM calculations on biomolecules or any other systems if you know their topologies. If you really want to use the internal QM/MM features of Q-Chem, you can try to build up your molecule using Tinker.
Let’s say that you have the PDB file of a protein. You can open the file with Tinker and choose a force field (from the Tinker’s library) to apply to the protein. Tinker will generate an input file for your system in the same format used for calculations in Q-Chem:
(element_symbol) (x) (y) (z) (atom_type) (bond_1) (bond_2) (bond_3) (bond_4)
A small warning: it can happen that Tinker makes mistakes in converting the PDB file into the Q-Chem input, especially if there are residue types or atom types in the PDB that are not in the Tinker’s library. Other mistakes can be related to the connectivity between atoms if the bonds are not explicitly listed already in the PDB.
The conclusion is that there is a way to generate molecules for QM/MM calculations in Q-Chem, but personally, it wouldn’t be my first choice. Life should be easier with one of the interfaces.