One assumption employed in the use of system-specific charges for proteins (and small molecules) is that the derived parameter set is not too dependent on the molecular conformation. To investigate this assumption, the sensitivity of the non-bonded parameters, for the GB3 protein, to the choice of input structure is investigated in Section S6.2. Ten structures were extracted from a MD simulation employing the OPLS-AA/M force field, and QUBE non-bonded parameters were computed for each snapshot. The standard deviation of the charge distribution across the ensemble is just 0.02 e, supporting previous observations that the underlying DDEC atoms-in-molecule charges are relatively independent of conformation. It is important to test whether these system-specific force field parameters translate into more accurate protein interactions and dynamics. In this regard, although the conformational preferences of the peptides tested in the previous section are promising, it is not known whether the torsional parameters will continue to be appropriate for use with proteins. As the non-bonded parameters vary with the system studied, the transferability of torsional parameters cannot be readily assumed. To assess this we begin by studying MD simulations of the proteins ubiquitin and GB3.