prac1autok分子对接实例练习.pptVIP

成功结束： Closing the docking parameter file (DPF)... This docking finished at: 1:13 13 p.m., 08/26/2010 ___________________________________________________ autodock4: Successful Completion on 4d6a3c1f806d462 Real= 11m 01.10s, CPU= 10m 53.44s, System= 0.75s 结果分析： 读入Docking Logs：ind.dlg , 其中有详细的对接记录. 用ind.dlg’读入前面进行的docking of the clinically-approved HIV-1 protease inhibitor, Indinavir, to protease. It contains many details that are output as AutoDock parses the input files and reports what it finds. For example, when AutoDock opens each AutoGrid map, it reports opening the map file and how many data points it read in. When it parses the input ligand file, it reports building various internal data structures. After the input phase, AutoDock begins the specified number of runs. It reports which run number it is starting; it may report specifics about each generation or simulated annealing cycle. After completing the runs, AutoDock begins an analysis phase of the conformational similarity of the dockings. summary of the time taken and outputs the words ‘Successful Completion’. 输出细节 的level由参数outlev控制. 对于用LGA算法进行对接，建议用minimal output (‘outlev 0’) . 对接的关键结果是：每轮对接后的结构或构象, 这些对接后结构的能量和它们之间的相似性. 对接后结构的相似性用rmsd来度量, between the coordinates of the atoms and creating a clustering of the conformations based on these rmsd values. The docking results consist of the PDBQT of the Cartesian coordinates of the atoms in the docked molecule, along with the state variables that describe this docked conformation and position and docked energies. 1。显示版本号：AutoDock 4.2 Release 4.2.3. 2。SETTING UP DEFAULT PARAMETER LIBRARY 3。 PARSING INPUT DOCKING PARAMETER FILE ga_run 10轮：LAMARCKIAN GENETIC ALGORITHM DOCKING 分析：analysis # perform a ranked cluster analysis CLUSTER ANALYSIS OF CONFORMATIONS 最后：LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER 用Estimated Free Energy of Binding排序对接的配体及坐标 分析过程 1. Analyze －? Dockings －? Open… Choose ind.dlg. 读入一个docking log：