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Molecular docking technology is an important tool in computer-aided drug discovery and structure prediction for the protein-ligand complex. In this work, based on the analysis of the algorithm of the widely used the docking program AutoDock, we proposed a hybrid parallel method using the message passing interface (MPI) library. The modified programs were applied to dock the small molecule XK263 to its target HIV-1 protease with different number of processors. Docking results indicate that the parallel codes can make a good prediction of the XK263-protease complex structure. The obtained high quality parallel speedup and efficiency show the promising improvement of our method for future applications on structure prediction of protein complex and drug design.