Figure : A comparison of the QUBE and OPLS non-bonded parameters for ubiquitin. The regions circled in correspond to carbonyl carbon atoms, which are expected to be electron deficient and therefore require small A and B Lennard-Jones coefficients. Blue and dashed black lines represent lines of best fit and y = x respectively. The use of system-specific non-bonded parameters for biomolecular force fields allows for long-ranged polarization effects to be included, which is expected to improve the accuracy of the force field, particularly for measurements such as protein-ligand binding affinity that are sensitive to the electrostatic potential at the protein surface. A comparison of the QUBE and OPLS non-bonded parameters for ubiquitin is shown in Figure . Figures for the other proteins tested follow similar trends. As we have described, QUBE non-bonded parameters are derived directly from the QM partitioned electron density, and so, each atom has a unique charge and set of Lennard-Jones coefficients which depend on its environment. In contrast, the OPLS parameters are read from a library of atom types. The QUBE and OPLS charges correlate well with no clear outliers. As has previously been observed, the QUBE Lennard-Jones parameters show a far greater level of variation than OPLS (and most other force fields).