The preparation of atomistic models of apatite-collagen composite mimicking enamel at length scales in the range of 1-10 nanometers is outlined. This bio-composite is characterized by a peculiar interplay of the collagen triplehelix and the apatite crystal structure. Structural coherence is however only obtained after drastic rearrangements, namely the depletion of protein-protein hydrogen bonds and the incorporation of calcium triangles which are stabilized by salt-bridges with the collagen molecule. Starting from an isolated collagen triple helix and a single-crystalline apatite structure, a composite model is obtained by gradually merging the two components via an additional (hyperspace) coordinate. This approach allows smooth structural relaxation of both components whilst avoiding singularities in potential energy due to atomic overlap.