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北京石油化工学院2026年研究生招生接收调剂公告

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arthurii

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专业: 药物设计与药物信息

[交流] 【求助】Autogrid的时候Error2，修改了路径有一个乱码的错误

Running: autogrid4 -p E:\csb\temp\123.gpf
[Error 2]

选定autogrid4.exe后，运行是开始了，但是又有错误。

Running: E:\csb\temp\autogrid4.exe -p E:\csb\temp\123.gpf

   _______________________________________________________

__________//____________________________/////_________________/________
_________/__/____________/_____________/______________/_______/________
________/____/___________/_____________/______________________/________
________/____/__/_____/_/////___/////__/__////_/_///__/__////_/________
_______/______/_/_____/__/_____/_____/_/_____/_//___/_/_/____//________
_______////////_/_____/__/_____/_____/_/_____/_/______/_/_____/________
_______/______/_/____//__/___/_/_____/_/_____/_/______/_/____//________
_______/______/__////_/___///___/////___/////__/______/__////_/________

   _______________________________________________________

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

            ______________________________________
            |                                     |
            |          AutoGrid 4.2.1          |
            |                                     |
            |       Garrett M. Morris, TSRI    |
            |          Ruth Huey, TSRI          |
            |       David S. Goodsell, TSRI    |
            |       Arthur J. Olson, TSRI       |
            |                                     |
            |       (C) 1989-2009, TSRI          |
            | The Scripps Research Institute    |
            |______________________________________|

            ______________________________________
            |                                     |
            | Calculation of van der Waals, H-Bond,|
            | Electrostatic Potential Energy, &  |
            | Desolvation Free Energy Grid Maps  |
            |          for AutoDock          |
            | For help, email autodock@scripps.edu |
            |______________________________________|

                        $Revision: 1.71 $

Maximum number of maps that can be computed = 16 (defined by MAX_MAPS in "autocomm.h"

.

This file was created at: 11:51 31" a.m., 08/21/2009
               using: "zsu-7077a27a02a"

Setting up parameter library with AutoDock default Unbound_Same_As_Bound values.

Free energy coefficient for the van der Waals term = 0.1662

Free energy coefficient for the H-bonding term    = 0.1209

Free energy coefficient for the electrostatic term = 0.1406

Free energy coefficient for the desolvation term = 0.1322

Free energy coefficient for the torsional term    = 0.2983

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 = 0.025,
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 = 0.025,
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 = 0.027,
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 = 0.027,
At.frag.vol. = 22.449,  At.solv.par. = -0.002,
Hb R-eqm = 1.900,  weighted Hb epsilon = 0.604,
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 = 0.027,
At.frag.vol. = 22.449,  At.solv.par. = -0.002,
Hb R-eqm = 1.900,  weighted Hb epsilon = 0.604,
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 = 0.033,
At.frag.vol. = 17.157,  At.solv.par. = -0.003,
Hb R-eqm = 1.900,  weighted Hb epsilon = 0.604,
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 = 0.033,
At.frag.vol. = 17.157,  At.solv.par. = -0.003,
Hb R-eqm = 1.900,  weighted Hb epsilon = 0.604,
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 = 0.013,
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 = 0.145,
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 = 0.145,
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 = 0.033,
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 = 0.033,
At.frag.vol. = 33.510,  At.solv.par. = -0.002,
Hb R-eqm = 2.500,  weighted Hb epsilon = 0.121,
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 = 0.033,
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 = 0.046,
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 = 0.046,
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 = 0.091,
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 = 0.091,
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 = 0.145,
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 = 0.145,
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 = 0.091,
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 = 0.091,
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 = 0.065,
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 = 0.065,
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 = 0.091,
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

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

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.025,
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 "G" were initialised with the following default values:

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.025,
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 "GA" were initialised with the following default values:

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.025,
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 "J" were initialised with the following default values:

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.025,
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 "Q" were initialised with the following default values:

R-eqm = 4.00 Angstrom,  weighted epsilon = 0.025,
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

GPF> npts 40 44 54                      # num.grid points in xyz

Number of grid points in x-direction: 41
Number of grid points in y-direction: 45
Number of grid points in z-direction: 55

GPF> gridfld 1kf1_H9.maps.fld          # grid_data_file

/cygdrive/e/csb/temp/autogrid4: ERROR:  can't create grid dimensions data file 1kf1_H9.maps.fld

/cygdrive/e/csb/temp/autogrid4: ERROR:  Unsuccessful completion.

/cygdrive/e/csb/temp/autogrid4: ERROR:  can't create grid dimensions data file 1kf1_H9.maps.fld

/cygdrive/e/csb/temp/autogrid4: ERROR:  Unsuccessful completion.

试过很多个不同的文件，包括几个练习示例，都是这样。在另一台机上重新装了一次，把文件全部放在默认路劲也是一样。

用VINA可以运行，但是直接在ADT上就用不了。
PS：autogrid4文件是新下载的4.2 MG是1.5.2的

[ Last edited by lei0736 on 2009-11-25 at 13:29 ]

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1楼 2009-08-21 12:01:03

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gwdavid

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arthurii(金币+1):谢谢参与
yjcmwgk(金币+1,VIP+0):感谢交流 8-21 18:43
arthurii(金币+5,VIP+0):谢谢，我再试试先 8-22 08:31

楼主先试试之前的版本可不可以，我看了一下，想不出哪里有问题，都对。
你下一个4.0.1版的试试

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个人博客：[url]http://blog.sina.com.cn/gaiwei[/url]

2楼2009-08-21 15:32:10

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winterose_

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arthurii(金币+1):谢谢参与
yjcmwgk(金币+2,VIP+0):thankU 8-25 17:34
arthurii(金币+2,VIP+0):正准备这样子，但是MGL的卸载和更换有点麻烦的说…… 8-25 21:09

建议LZ将MGL换成1.5.4的版本,版本不对路很容易出错.
1.5.2对应的是4.0版本,1.5.4对应的是4.2.
换了以后所有的准备文件也要用新版本重新准备一遍,否则Grid没问题,Dock也会有问题地.

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3楼2009-08-25 16:56:42

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liujunhero

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arthurii(金币+1):谢谢参与
arthurii(金币+1,VIP+0):谢谢 8-25 21:09

估计是版本的兼容性问题

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4楼2009-08-25 20:43:05

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arthurii(金币+1):谢谢参与

祝福楼主啊

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5楼2009-08-26 02:35:55

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小木虫(金币+0.5):给个红包，谢谢回帖交流
yjcmwgk(金币+1,VIP+0): 10-15 16:30

你是在adt中做的吗？把参数文件、autodock4、autogrid4都放到c:\document and setting\usr下面，再运行autogrid4试试。

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6楼2009-10-14 22:36:38

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