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swordzj858至尊木虫 (著名写手)
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[交流]
【求助】Autodock4中的文件存放问题
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| 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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gwdavid
木虫 (著名写手)
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2楼2008-07-29 20:35:42
chemozhang
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3楼2008-07-31 00:25:09
4楼2008-09-03 15:40:50
suyuehua
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运行出错
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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 |
5楼2008-09-05 10:45:54
gwdavid
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6楼2008-09-05 13:03:42
suyuehua
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7楼2008-09-13 17:33:11
suyuehua
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8楼2008-09-13 17:34:10
