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.