The effective interaction between two dendrimer molecules has been calculated from pairs of conformations, generated by Monte Carlo simulations, for coarse-grained models of PPI-DAB and PAMAM-EDA of different generation numbers (g = 2 to 7). The resulting interaction curves are compared with a theoretical Gaussian function. It is shown that the different simulation data can be adequately fitted to Gaussian functions in the relevant range of overlapping distances, but the fitting parameters are significantly different from those predicted by the theory for the highest values of g (which exhibit stronger interactions). Assuming a solvent mediated potential, the theoretical and Monte Carlo generated interaction curves are employed in molecular dynamics calculations of structure factors for different PPI-DAB dendrimer solutions having different concentrations. These calculations demonstrate that the different theoretical and simulation interactions may lead to significantly different quantitative and qualitative predictions for structural properties of dendrimer systems. Larger dendrimer molecules may be adequately described according to the observed trends in the parameter variations with generation number for these types of dendrimers.