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In this paper we describe a mathematical and numerical approach that combines physics-based simulated ground motion caused by earthquakes with fragility functions to model the structural damages induced to buildings. To simulate earthquake ground motion we use the discontinuous Galerkin spectral element method to solve a three-dimensional differential model at regional scale describing the propagation of seismic waves through the earth layers up to the surface. Selected intensity measures, retrieved from the synthetic time histories, are then employed as input for a vulnerability model based on fragility functions, in order to predict building damage scenarios at urban scale. The main features and effectiveness of the proposed numerical approach are tested on the Beijing metropolitan area.