We discuss some limitations of combined quantum mechanics and molecular mechanics methods, which are becoming popular when working with large chemical and biochemical systems. More precisely, we focus on the treatment of the short-range interaction between a quantum molecule and a classical system. Generally, this short-range energy is handled by a sum over atom pairs of A/R-12 terms, where R is the atom-atom separation, as in Lennard-Jones potentials. We illustrate the limitations of this approach and propose two other methods. The first one consists in the use of a Buckingham-type formula which, compared to the A/R-12 term, is mathematically more flexible and physically more adequate. The second one is based on the use of a pseudopotential for describing the classical atoms that interact with the electronic cloud of the quantum system. The transferability of these potentials is discussed.