Autodock程序使用方法

采用LoadLever作业脚本方式提交作业，用户需要修改输入序列和需要比对的数据库，及需要运行的节点数和每节点任务数。

[loadl@f01n01 /gpfs/home/loadl/lltest/autodock]$vi autodock.cmd

#!/usr/bin/bash

# @ error   = autodock.$(Host).$(jobid).err

# @ output  = autodock.$(Host).$(jobid).out

# @ requirements = (Pool == 1)

# @ initialdir = /gpfs/home/loadl/lltest/autodock/test

# @ queue

/gpfs/application/autodock/autodock4 -p jff.dpf -l jff.dlg

运行如下命令提交作业：

[loadl@cams /gpfs/home/loadl/lltest/autodock]$ llsubmit autodock.cmd

llsubmit: The job "f01n01.294" has been submitted.

作业成功提交后可以看到系统返回的作业编号" f01n01.294"。

通过llq命令可以查看作业状态：

[loadl@cams /gpfs/home/loadl/lltest/autodock]$ llq

Id                       Owner      Submitted   ST PRI Class        Running on

------------------------ ---------- ----------- -- --- ------------ -----------

cams.214.0               loadl       1/15 16:12 R  50  small        f01n05

1 job step(s) in queue, 0 waiting, 0 pending, 1 running, 0 held, 0 preempted

作业运行完毕后，结果可以在输出文件中查看：

[loadl@f01n01 /gpfs/home/loadl/lltest/autodock]$ head -n 80 test/jff.dlg

      ________________________________________________________________

__________//___________________________/////___________________/____________

_________/__/__________________________/____/__________________/____________

________/____/___________/_____________/_____/_________________/____________

________/____/__/_____/_/////___/////__/_____/__/////___/////__/___/________

_______/______/_/_____/__/_____/_____/_/_____/_/_____/_/_____/_/_//_________

_______////////_/_____/__/_____/_____/_/_____/_/_____/_/_______//_/_________

_______/______/_/____//__/___/_/_____/_/____/__/_____/_/_____/_/___/________

_______/______/__////_/___///___/////__/////____/////___/////__/____/_______

      ________________________________________________________________

                                ______

                               /      \

                              /        \

                             /          \

                             \\    /\\    /

                              \\  /  \\  /

                               \/ /\\ \/

                                 /  \

                                /____\

                  ______________________________________

                 |                                      |

                 |            AutoDock 4.00             |

                 |                                      |

                 |            (c) 1991-2007             |

                 |    The Scripps Research Institute    |

                 |                                      |

                 |       Garrett M. Morris, TSRI        |

                 |            Ruth Huey, TSRI           |

                 |        William E. Hart, Sandia       |

                 |        William Lindstrom, TSRI       |

                 |        Alexander Gillet, TSRI        |

                 |       David S. Goodsell, TSRI        |

                 |        Arthur J. Olson, TSRI         |

                 |______________________________________|

                  ______________________________________

                 |                                      |

                 | Automated Docking of Flexible Ligand |

                 |  to Flexible Macromolecular Receptor |

                 |______________________________________|

        AutoDock comes with ABSOLUTELY NO WARRANTY; for details

        type 'warranty'.  This is free software, and you are welcome

        to redistribute it under certain conditions; type 'copyright'

        for details.

                           $Revision: 1.69 $

                   Compiled on Dec 18 2008 at 10:24:00

This file was created at:                       4:12 56" p.m., 01/15/2009

                   using:                       "f01n05"

NOTE: "rus" stands for:

      r = Real, wall-clock or elapsed time;

      u = User or cpu-usage time;

      s = System time

All timings are in seconds, unless otherwise stated.

      ________________________________________________________________

                   SETTING UP DEFAULT PARAMETER LIBRARY

      ________________________________________________________________

Setting up parameter library with factory default values.

完整结果可以查看 jff.dlg