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swordzj858

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[交流] 【求助】Autodock4中的文件存放问题

请教各位高手，我用的是Windows版本的Autodock4.0，是AutoDockTools1.5.2工具，请问这是不是要求把配体和受体的相关文件必须放在固定的文件夹下呢？如果是，请问文件夹的路径是什么？我随便放在一个文件夹下，但是最后一步运行Run-Autodock4时一直出现问题。请各位高手指教。

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1楼 2008-07-29 15:51:36

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gwdavid

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★ ★ ★ ★
swordzj858(金币+2,VIP+0):Thanks
zzgyb(金币+2,VIP+0):谢谢你的参与，欢迎再次光临计算模拟版！

是的，autodock4和autogrid4必须放在同一个文件夹下，而且如果你要从ADT来启动计算的话，由于它带路径运行不成功，所以建议你在用ADT准备好文件之后，在命令行直接输入命令来运行，这很简单。
而如果你实在要用ADT来运行的话，试着将preferences中的启动路径改为你要运行的当前路径，然后在对话框中不要带任何路径

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2楼2008-07-29 20:35:42

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chemozhang

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zzgyb(金币+1,VIP+0):谢谢你的参与，欢迎再次光临计算模拟版！

准备文件必需全部放在同一个文件夹,
楼上的以说的很详细

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3楼2008-07-31 00:25:09

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huchiwen

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不是随便放在同一个文件夹里就可以的吧“？我以前开始全都放到桌面上，可是不行。后来别人说要放到C:\Documents and Settings\Administrator才行。我的确是这样才行哦。
我也是新手，呵呵。

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4楼2008-09-03 15:40:50

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suyuehua

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运行出错

高手看一下,有何问题,如何更改.

Running: D:\Documents and Settings\Administrator\autodock4.exe -p D:\Documents and Settings\Administrator\ind.dpf
   ________________________________________________________________

__________//___________________________/////___________________/____________
_________/__/__________________________/____/__________________/____________
________/____/___________/_____________/_____/_________________/____________
________/____/__/_____/_/////___/////__/_____/__/////___/////__/___/________
_______/______/_/_____/__/_____/_____/_/_____/_/_____/_/_____/_/_//_________
_______////////_/_____/__/_____/_____/_/_____/_/_____/_/_______//_/_________
_______/______/_/____//__/___/_/_____/_/____/__/_____/_/_____/_/___/________
_______/______/__////_/___///___/////__/////____/////___/////__/____/_______

   ________________________________________________________________

                              ______
                           /    \
                           /       \
                           /       \
                           \ /\ /
                           \  /  \  /
                           \/ /\ \/
                              /  \
                              /____\

               ______________________________________
               |                                     |
               |          AutoDock 4.00          |
               |                                     |
               |          (c) 1991-2006          |
               | 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 |
               |______________________________________|

                        $Revision: 1.66 $

               Compiled on Apr  3 2007 at 04:34:55

This file was created at: 10:34 27" a.m., 09/05/2008
               using: "acer-74061b0468"

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.

Free energy coefficient for the van der Waals term = 0.1560

Free energy coefficient for the H-bonding term    = 0.0974

Free energy coefficient for the electrostatic term = 0.1465

Free energy coefficient for the desolvation term = 0.1159

Free energy coefficient for the torsional term    = 0.2744

Parameters for the atom type "H" were initialised with the following default values:

R-eqm = 2.00 Angstrom,  weighted epsilon = 0.003,
At.frag.vol. = 0.000,  At.solv.par. = 0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 3

Parameters for the atom type "HD" were initialised with the following default values:

R-eqm = 2.00 Angstrom,  weighted epsilon = 0.003,
At.frag.vol. = 0.000,  At.solv.par. = 0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 2,  bond index = 3

Parameters for the atom type "HS" were initialised with the following default values:

R-eqm = 2.00 Angstrom,  weighted epsilon = 0.003,
At.frag.vol. = 0.000,  At.solv.par. = 0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 1,  bond index = 3

Parameters for the atom type "C" were initialised with the following default values:

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.023,
At.frag.vol. = 33.510,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 0

Parameters for the atom type "A" were initialised with the following default values:

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.023,
At.frag.vol. = 33.510,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 0

Parameters for the atom type "N" were initialised with the following default values:

R-eqm = 3.50 Angstrom,  weighted epsilon = 0.025,
At.frag.vol. = 22.449,  At.solv.par. = -0.002,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 1

Parameters for the atom type "NA" were initialised with the following default values:

R-eqm = 3.50 Angstrom,  weighted epsilon = 0.025,
At.frag.vol. = 22.449,  At.solv.par. = -0.002,
Hb R-eqm = 1.900,  weighted Hb epsilon = 0.487,
Hb type = 4,  bond index = 1

Parameters for the atom type "NS" were initialised with the following default values:

R-eqm = 3.50 Angstrom,  weighted epsilon = 0.025,
At.frag.vol. = 22.449,  At.solv.par. = -0.002,
Hb R-eqm = 1.900,  weighted Hb epsilon = 0.487,
Hb type = 3,  bond index = 1

Parameters for the atom type "OA" were initialised with the following default values:

R-eqm = 3.20 Angstrom,  weighted epsilon = 0.031,
At.frag.vol. = 17.157,  At.solv.par. = -0.003,
Hb R-eqm = 1.900,  weighted Hb epsilon = 0.487,
Hb type = 5,  bond index = 2

Parameters for the atom type "OS" were initialised with the following default values:

R-eqm = 3.20 Angstrom,  weighted epsilon = 0.031,
At.frag.vol. = 17.157,  At.solv.par. = -0.003,
Hb R-eqm = 1.900,  weighted Hb epsilon = 0.487,
Hb type = 3,  bond index = 2

Parameters for the atom type "F" were initialised with the following default values:

R-eqm = 3.09 Angstrom,  weighted epsilon = 0.012,
At.frag.vol. = 15.448,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "Mg" were initialised with the following default values:

R-eqm = 1.30 Angstrom,  weighted epsilon = 0.137,
At.frag.vol. = 1.560,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "MG" were initialised with the following default values:

R-eqm = 1.30 Angstrom,  weighted epsilon = 0.137,
At.frag.vol. = 1.560,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "P" were initialised with the following default values:

R-eqm = 4.20 Angstrom,  weighted epsilon = 0.031,
At.frag.vol. = 38.792,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 5

Parameters for the atom type "SA" were initialised with the following default values:

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.031,
At.frag.vol. = 33.510,  At.solv.par. = -0.002,
Hb R-eqm = 2.500,  weighted Hb epsilon = 0.097,
Hb type = 5,  bond index = 6

Parameters for the atom type "S" were initialised with the following default values:

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.031,
At.frag.vol. = 33.510,  At.solv.par. = -0.002,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 6

Parameters for the atom type "Cl" were initialised with the following default values:

R-eqm = 4.09 Angstrom,  weighted epsilon = 0.043,
At.frag.vol. = 35.824,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "CL" were initialised with the following default values:

R-eqm = 4.09 Angstrom,  weighted epsilon = 0.043,
At.frag.vol. = 35.824,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "Ca" were initialised with the following default values:

R-eqm = 1.98 Angstrom,  weighted epsilon = 0.086,
At.frag.vol. = 2.770,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "CA" were initialised with the following default values:

R-eqm = 1.98 Angstrom,  weighted epsilon = 0.086,
At.frag.vol. = 2.770,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "Mn" were initialised with the following default values:

R-eqm = 1.30 Angstrom,  weighted epsilon = 0.137,
At.frag.vol. = 2.140,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "MN" were initialised with the following default values:

R-eqm = 1.30 Angstrom,  weighted epsilon = 0.137,
At.frag.vol. = 2.140,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "Fe" were initialised with the following default values:

R-eqm = 1.30 Angstrom,  weighted epsilon = 0.002,
At.frag.vol. = 1.840,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "FE" were initialised with the following default values:

R-eqm = 1.30 Angstrom,  weighted epsilon = 0.002,
At.frag.vol. = 1.840,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "Zn" were initialised with the following default values:

R-eqm = 1.48 Angstrom,  weighted epsilon = 0.086,
At.frag.vol. = 1.700,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "ZN" were initialised with the following default values:

R-eqm = 1.48 Angstrom,  weighted epsilon = 0.086,
At.frag.vol. = 1.700,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "Br" were initialised with the following default values:

R-eqm = 4.33 Angstrom,  weighted epsilon = 0.061,
At.frag.vol. = 42.566,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "BR" were initialised with the following default values:

R-eqm = 4.33 Angstrom,  weighted epsilon = 0.061,
At.frag.vol. = 42.566,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Parameters for the atom type "I" were initialised with the following default values:

R-eqm = 4.72 Angstrom,  weighted epsilon = 0.086,
At.frag.vol. = 55.059,  At.solv.par. = -0.001,
Hb R-eqm = 0.000,  weighted Hb epsilon = 0.000,
Hb type = 0,  bond index = 4

Preparing Energy Tables for Bound Calculation:

Calculating distance-dependent dielectric function using the method of Mehler & Solmajer

Preparing Energy Tables for Unbound Calculation:

Calculating distance-dependent dielectric function using the method of Mehler & Solmajer

   ___________________________________________________

         PARSING INPUT DOCKING PARAMETER FILE
   ___________________________________________________

Docking parameter file (DPF) used for this docking: D:\Documents and Settings\Administrator\ind.dpf

DPF> outlev 1                            # diagnostic output level

Output Level = 1.  MINIMUM OUTPUT DURING DOCKING.

Output every 100 generations.

DPF> parameter_file AD4.1_bound.dat    # parameter library filename

Sorry, I can't find or open AD4.1_bound.dat
Using read_parameter_library

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5楼2008-09-05 10:45:54

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gwdavid

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在你的MGLTools的安装文件夹中有AD4.1_bound.dat这个文件,你找到它后,将他copy到你的对接文件所在目录就可以了

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6楼2008-09-05 13:03:42

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suyuehua

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clean up

PDB 文件变成PDBQT变成前,一定要clean up吗?应当用何软件处理.

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7楼2008-09-13 17:33:11

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suyuehua

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clean up

PDB 文件变成PDBQT文件前,一定要clean up吗?应当用何软件处理.

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8楼2008-09-13 17:34:10

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相关版块跳转我要订阅楼主 swordzj858 的主题更新

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