Methodologies that combine quantum and classical mechanics (QM/MM) are now widely used to study chemical problems in proteins. A small part of the protein (e.g. an amino acid, a side-chain, etc.) is treated quantum mechanically while the remaining part is treated using a classical force-field. The widely used ‘Link Atom’ scheme (LA) allows to saturate the QM part in a straightforward and easy fashion. This article shows some limitations of the LA scheme (at the ab initio level) when this is applied to systems containing an amide bond that is—or that is close—to the QM/MM frontier. As expected, the ‘invisibility’ of the link atom from the MM side introduces severe over-polarization effects due to non-balanced interactions. Moreover, in some cases, the resulting QM/MM wavefunction seems unstable with respect to a closed shell→open shell relaxation.