To achieve our goal of employing the QUBE force field in computer-aided drug design applications, we require a compatible protein force field. Since the non-bonded parametrization strategy employed in QUBE is very different to that used in the standard biomolecular force fields (e.g. AMBER, OPLS, CHARMM), there is no reason to believe that they are compatible. However, by implementing the atoms-in-molecule non-bonded parameter derivation methods in the ONETEP linear-scaling density functional theory (DFT) software, we have shown that it is feasible to derive these charges and Lennard-Jones parameters for entire proteins. In this way, the number of fitting parameters is substantially reduced, and we have a consistent parametrization approach that can be applied to both small and large molecules, including entire biomolecular assemblies. Since, in this approach, all non-bonded parameters are derived from a single QM calculation, both the charge and Lennard-Jones parameters naturally include the native state polarization effects of the environment. Importantly, we have shown that protein charges derived using DDEC electron density partitioning recreate the underlying QM electrostatic potential with high accuracy, and that charges derived for a NMR ensemble of BPTI protein structures are not too conformation-dependent (standard deviations per residue less than 0.04 e). This is in contrast to the performance of RESP charges, which have been shown to be significantly more conformation-dependent for an ensemble of polypeptide structures. Additional simulations demonstrated the feasibility and advantages of deriving bespoke parameters for a protein-ligand complex. The computed relative binding free energy of indole and benzofuran to the lysozyme protein using the environment-specific force fields (-0.4 kcal/mol) was in excellent agreement with experiment (-0.6 kcal/mol), and was substantially more accurate than standard force fields (-2.4 kcal/mol). However, the force field was in need of further development as the bespoke non-bonded terms were used in combination with standard OPLS-AA bonded parameters.