We have shown how relative binding free energy (RBFE) techniques can be applied to large protein complexes to predict, with some success, the effect of individual protein mutations on the binding of an antibiotic, and thence whether resistance is conferred. When the size of the signal is large and the mutations do not involve significant changes in the electrical charge, as is the case for the rpoB mutations, one can successfully predict whether a mutation confers resistance to the antibiotic (in this case rifampicin). If the fold increase in minimum inhibitory concentration is small and/or there are significant charge changes, as is the case for most of the resistance conferring mutations in the DNA gyrase, then the estimated error of DDG will likely be so large that no definite prediction can be made. In addition, the observed non-normality of the DG qon free energy for gyrA D94G indicates that these values are also not independent: to solve this either the λ simulations would have to be extended or the equilibration simulations would need to be more numerous as well as longer.