A　docking　approach　is　proposed　for　the　prediction　of　the　interaction　of　HIV-1　integrase　(IN)　and　inhibitor　aurintricarboxylic　acid.　In　order　to　clarify　the　function　of　metal　ions　on　the　binding　process,　we　chose　two　kinds　of　integrase　receptors　(one　with　an　Mg+2　and　another　without　Mg+2)　and　performed　docking　with　aurintricarboxylic　acid　respectively.　The　receptor　structure　used　for　docking　was　made　by　the　following　processes.　Because　there　is　no　report　on　the　three-dimensional　structure　of　IN/aurintricarboxylic　acid　complex,　the　only　known　crystals　structure　of　the　complex　of　the　HIV-1　integrase　core　domain　with　an　inhibitor　5CITEP(PDB　code　1　QS4)　was　referenced,　and　the　monomer　coordinate(　chain　A)　was　selected.　Then,　the　lacked　residues　from　number　141　to　144　were　added　by　using　Insight　II.　The　final　structure　after　200　ps　molecular　dynamics　simulation　was　used　as　the　receptor　structure　for　docking.　The　flexibility　of　the　small　molecule　was　allowed　through　rotating　its　dihedrals.　The　genetic　algorithm　was　used　and　the.　empirical　potential　was　taken　as　an　energy　score　function　when　docking　was　being　done..　All　possible　conformations　were　searched　throughout　the　full　configuration　space.　The　results　of　our　study　illustrate　that　the　ion　Mg+2　is　important　for　the　stability　of　the　binding　of　the　ligand　and　receptor.　In　the　case　of　ligand　aurintricarboxylic　acid　docked　with　integrase　with　an　Mg+2,　the　minimized　binding　free　energy　is　-45.　19　kJ/mol.　It　is　found　that　the　water　molecules　located　in　the　active　site　are　substituted　by　the　carbonyl　oxygen　atoms　of　aurintricarboxylic　acid,　and　the　two　oxygen　atoms　in　the　carboxy　group　of　aurintricarboxylic　acid　can　form　a　hexahedral　ligand　structure　with　the　two　oxygen　atoms　of　Asp64　and　Asp116.　Thus,　the　complex　has　a　much　more　stable　structure　with　low　energy　due　to　a　salt　bond　interaction　between　aurintricarboxylic　acid　and　Mg+2.　When　the　Mg+2　is　lost,　the　configuration　of　integrase　in　the　active　site　will　be　changed,　which　makes　the　binding　free　energy　(-　24.　35　kJ/mol)　increase　distinctly.　In　the　present　study　the　unknown　complex　structure　of　HIV-1　integrase　and　its　inhibitor　aurintricarboxylic　acid　has　been　predicted,　which　may　offer　significant　information　on　the　drug　design　of　the　anti　HIV-1　integrase　based　on　structure.