We estimate a bedrock motion on the Rokko granite rock from the record observed at the JMA Kobe station during the Hyogo-ken Nambu earthquake of 1995 and use it to simulate strong motions in the Sannomiya district in Chuo Ward, Kobe, where heavily damaged buildings were concentrated. We use a two-dimensional finite element method to model local topography, shallow sub-surface layers, and a deep basin structure formed by the Rokko faults. The inverted bedrock motion has a peak ground acceleration of 335 cm/sec^2 and a velocity of 55 cm/sec. Then we calculate responses of the Sannomiya ground model without holocene layers assuming most plausible, linear soil constants. The resultant ground motions have peak accelerations or velocities well exceeding 800 cm/sec^2 or 100 cm/sec, respectively, in the narrow zone 750m away from the fault. These peak values could be more on the surface since holocene layers would amplify them. We verified our scheme by comparing the results of nonlinear analysis with the borehole records observed at the Port Island, one of reclaimed islands in Kobe. These results suggest that both a deep basin structure and shallow holocene layers have to be taken into account to simulate the strong ground motions and hence to explain damage concentration in Kobe during the Hyogo-ken Nambu earthquake.