Molecular docking technology is an important tool in molecular recognition and structure prediction for the protein-protein complex. In this work, based on the analysis of the widely used FFT-based method, we proposed a GPU parallel molecular docking program. The new docking program was applied to dock 5 protein-protein complexes of enzyme/inhibitor type. Docking results indicate that the parallel codes can make a good prediction of the given complex structures. Moreover, the GPU docking method can achieve a speedup of more than 3 times. Finally, we analyzed the influence of parameters for the docking results and parallel speedup. The obtained high quality parallel speedup and efficiency show the promising improvement of our method for future applications on structure prediction of protein-protein complex.