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dongdyp金虫 (正式写手)
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【求助】autogrid4运行错误
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严格按照中文操作手册实行，中间并未发现任何异常，最后却说打不开相关文件，请高人指点 Running: autogrid4 -p C:\Python25\Lib\site-packages\MGLToolsPckgs\AutoDockTools\bin\my project\3B9N.gpf _______________________________________________________ __________//____________________________/////_________________/________ _________/__/____________/_____________/______________/_______/________ ________/____/___________/_____________/______________________/________ ________/____/__/_____/_/////___/////__/__////_/_///__/__////_/________ _______/______/_/_____/__/_____/_____/_/_____/_//___/_/_/____//________ _______////////_/_____/__/_____/_____/_/_____/_/______/_/_____/________ _______/______/_/____//__/___/_/_____/_/_____/_/______/_/____//________ _______/______/__////_/___///___/////___/////__/______/__////_/________ _______________________________________________________ ______ / \ / \ / \ \ /\ / \ / \ / \/ /\ \/ / \ /____\ ______________________________________ | | | AutoGrid 4.2.2 | | | | 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: 1.72 $ Maximum number of maps that can be computed = 16 (defined by MAX_MAPS in "autocomm.h"  .This file was created at: 4:16 01" p.m., 12/01/2009 using: "192bc95cf405430" 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> receptor 3B9N.pdbqs # macromolecule autogrid4: ERROR: can't find or open receptor PDBQT file "3B9N.pdbqs". autogrid4: ERROR: Unsuccessful completion. Receptor Input File : 3B9N.pdbqs Receptor Atom Type Assignments: autogrid4: ERROR: can't find or open receptor PDBQT file "3B9N.pdbqs". autogrid4: ERROR: Unsuccessful completion. [ Last edited by dongdyp on 2009-12-1 at 17:14 ] |
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3楼2009-12-07 15:53:19
javacfish
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找不到"3B9N.pdbqs". 先按照我这个例子在运行一遍。 http://download.csdn.net/source/1863350 里面有运行完的实例，你比较一下吧 |
2楼2009-12-01 17:21:23
arthurii
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4楼2009-12-08 12:38:39
5楼2009-12-09 15:33:47