________________________________________________________________ __________//___________________________/////___________________/____________ _________/__/__________________________/____/__________________/____________ ________/____/___________/_____________/_____/_________________/____________ ________/____/__/_____/_/////___/////__/_____/__/////___/////__/___/________ _______/______/_/_____/__/_____/_____/_/_____/_/_____/_/_____/_/_//_________ _______////////_/_____/__/_____/_____/_/_____/_/_____/_/_______//_/_________ _______/______/_/____//__/___/_/_____/_/____/__/_____/_/_____/_/___/________ _______/______/__////_/___///___/////__/////____/////___/////__/____/_______ ________________________________________________________________ ______ / \ / \ / \ \ /\ / \ / \ / \/ /\ \/ / \ /____\ ______________________________________ | | | 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 May 18 2007 at 02:57:27 This file was created at: 11:01 02" p.m., 02/22/1970 using: "mac-90023.lal.in2p3.fr" 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: Preparing Energy Tables for Unbound Calculation: ___________________________________________________ PARSING INPUT DOCKING PARAMETER FILE ___________________________________________________ Docking parameter file (DPF) used for this docking: ./1pgp.dpf DPF> outlev 0 Output Level = 0. Output every 30000 generations. DPF> parameter_file AD4_parameters.dat # New parameter library >>> NEW Using read_parameter_library 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 "C" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "OS" were read in from "AD4_parameters.dat" as follows: 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 "SA" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "H" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "P" were read in from "AD4_parameters.dat" as follows: 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 "Br" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "Ca" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "Cl" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "F" were read in from "AD4_parameters.dat" as follows: 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 "Fe" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "I" were read in from "AD4_parameters.dat" as follows: 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 Parameters for the atom type "Mg" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "Mn" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 "Zn" were read in from "AD4_parameters.dat" as follows: 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 read in from "AD4_parameters.dat" as follows: 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 DPF> #include_1_4_interactions 1.0 # test >>> NEW DPF> intelec # calculate internal electrostatic energy Electrostatic energies will be calculated for all non-bonds between moving atoms. DPF> DPF> # seed pid time # seeds for random generator DPF> seed 28641 1106107140 # seeds for random generator 2 seeds found. argument "28641" found argument "1106107140" found Random number generator was seeded with the user-specified value 28641 Random number generator was seeded with the user-specified value 1106107140 Portable random number generator was seeded with the user-specified values 28641, 1106107140 DPF> DPF> ligand_types C HD OA P # ligand atom type names >>> NEW Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for C-C interactions, used in internal energy calculations: 392586.8 191.7 E = ----------- - ----------- C,C 12 6 r r Calculating C-C interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for C-C interactions, used in unbound energy calculations: 392586.8 E = ----------- - r C,C 12 r Calculating C-C interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.01 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for C-HD and HD-C interactions, used in internal energy calculations: 4540.9 12.5 E = ----------- - ----------- C,HD 12 6 r r Calculating C-HD interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.01, CPU= 0.01, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for C-HD and HD-C interactions, used in unbound energy calculations: 392586.8 E = ----------- - r C,HD 12 r Calculating C-HD interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for C-OA and OA-C interactions, used in internal energy calculations: 128031.0 117.6 E = ----------- - ----------- C,OA 12 6 r r Calculating C-OA interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for C-OA and OA-C interactions, used in unbound energy calculations: 392586.8 E = ----------- - r C,OA 12 r Calculating C-OA interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.01, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for C-P and P-C interactions, used in internal energy calculations: 609665.2 256.7 E = ----------- - ----------- C,P 12 6 r r Calculating C-P interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.01, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for C-P and P-C interactions, used in unbound energy calculations: 392586.8 E = ----------- - r C,P 12 r Calculating C-P interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for HD-HD interactions, used in internal energy calculations: 12.8 0.4 E = ----------- - ----------- HD,HD 12 6 r r Calculating HD-HD interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.01, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for HD-HD interactions, used in unbound energy calculations: 392586.8 E = ----------- - r HD,HD 12 r Calculating HD-HD interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.01, System= 0.00 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for HD-OA and OA-HD interactions, used in internal energy calculations: 5389.4 1791.5 E = ----------- - ----------- HD,OA 12 10 r r Calculating HD-OA interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for HD-OA and OA-HD interactions, used in unbound energy calculations: 392586.8 E = ----------- - r HD,OA 12 r Calculating HD-OA interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for HD-P and P-HD interactions, used in internal energy calculations: 7771.3 17.5 E = ----------- - ----------- HD,P 12 6 r r Calculating HD-P interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.01, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for HD-P and P-HD interactions, used in unbound energy calculations: 392586.8 E = ----------- - r HD,P 12 r Calculating HD-P interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.01, System= 0.00 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for OA-OA interactions, used in internal energy calculations: 35971.2 67.0 E = ----------- - ----------- OA,OA 12 6 r r Calculating OA-OA interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for OA-OA interactions, used in unbound energy calculations: 392586.8 E = ----------- - r OA,OA 12 r Calculating OA-OA interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.01, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for OA-P and P-OA interactions, used in internal energy calculations: 205388.1 160.1 E = ----------- - ----------- OA,P 12 6 r r Calculating OA-P interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.01, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for OA-P and P-OA interactions, used in unbound energy calculations: 392586.8 E = ----------- - r OA,P 12 r Calculating OA-P interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for docking calculation; Non-bonded parameters for P-P interactions, used in internal energy calculations: 940038.9 342.5 E = ----------- - ----------- P,P 12 6 r r Calculating P-P interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.00, CPU= 0.00, System= 0.00 Calculating internal non-bonded interaction energies for unbound conformation calculation; Non-bonded parameters for P-P interactions, used in unbound energy calculations: 392586.8 E = ----------- - r P,P 12 r Calculating P-P interaction energy versus atomic separation (2048 data points). Time taken: Real= 0.01, CPU= 0.00, System= 0.00 DPF> fld 1pgp_rec.maps.fld # grid_data_file Opening Grid Map Dimensions file: 1pgp_rec.maps.fld Grid Point Spacing = 0.375 Angstroms Even Number of User-specified Grid Points = 40 x-points 40 y-points 40 z-points Adding the Central Grid Point makes: 41 x-points 41 y-points 41 z-points Coordinates of Central Grid Point of Maps = (23.503, 29.451, 39.784) Macromolecule file used to create Grid Maps = 1pgp_rec.pdbqt Grid Parameter file used to create Grid Maps = 1pgp.gpf Minimum coordinates in grid = (16.003, 21.951, 32.284) Maximum coordinates in grid = (31.003, 36.951, 47.284) DPF> map 1pgp_rec.C.map # atom-specific affinity map Opened Grid Map 1 (C): 1pgp_rec.C.map Checking header information. Number of grid points expected in x-dimension: 41 Number of grid points expected in y-dimension: 41 Number of grid points expected in z-dimension: 41 Looking for 68921 energies from Grid Map 1... Closing file. 68921 energies found for map 1 Minimum energy = -0.85, maximum energy = 202315.86 Time taken (s): Real= 0.25, CPU= 0.20, System= 0.05 Min= -0.853 Mean= 15840.843 Max= 202315.859 DPF> map 1pgp_rec.HD.map # atom-specific affinity map Opened Grid Map 2 (HD): 1pgp_rec.HD.map Checking header information. Number of grid points expected in x-dimension: 41 Number of grid points expected in y-dimension: 41 Number of grid points expected in z-dimension: 41 Looking for 68921 energies from Grid Map 2... Closing file. 68921 energies found for map 2 Minimum energy = -0.59, maximum energy = 106529.91 Time taken (s): Real= 0.19, CPU= 0.19, System= 0.00 Min= -0.592 Mean= 3630.208 Max= 106529.914 DPF> map 1pgp_rec.OA.map # atom-specific affinity map Opened Grid Map 3 (OA): 1pgp_rec.OA.map Checking header information. Number of grid points expected in x-dimension: 41 Number of grid points expected in y-dimension: 41 Number of grid points expected in z-dimension: 41 Looking for 68921 energies from Grid Map 3... Closing file. 68921 energies found for map 3 Minimum energy = -1.37, maximum energy = 200226.69 Time taken (s): Real= 0.20, CPU= 0.19, System= 0.01 Min= -1.372 Mean= 11342.202 Max= 200226.688 DPF> map 1pgp_rec.P.map # atom-specific affinity map Opened Grid Map 4 (P): 1pgp_rec.P.map Checking header information. Number of grid points expected in x-dimension: 41 Number of grid points expected in y-dimension: 41 Number of grid points expected in z-dimension: 41 Looking for 68921 energies from Grid Map 4... Closing file. 68921 energies found for map 4 Minimum energy = -1.00, maximum energy = 204084.52 Time taken (s): Real= 0.20, CPU= 0.19, System= 0.00 Min= -0.996 Mean= 18241.490 Max= 204084.516 DPF> elecmap 1pgp_rec.e.map # electrostatics map Opened Grid Map 5 (e): 1pgp_rec.e.map Checking header information. Number of grid points expected in x-dimension: 41 Number of grid points expected in y-dimension: 41 Number of grid points expected in z-dimension: 41 Looking for 68921 energies from Grid Map 5... Closing file. 68921 energies found for map 5 Minimum electrostatic potential = -33.54, maximum electrostatic potential = 32.64 Time taken (s): Real= 0.19, CPU= 0.18, System= 0.01 Min= -33.539 Mean= 0.570 Max= 32.643 DPF> desolvmap 1pgp_rec.d.map # desolvation map Opened Grid Map 6 (d): 1pgp_rec.d.map Checking header information. Number of grid points expected in x-dimension: 41 Number of grid points expected in y-dimension: 41 Number of grid points expected in z-dimension: 41 Looking for 68921 energies from Grid Map 6... Closing file. 68921 energies found for map 6 Minimum energy = 0.07, maximum energy = 1.36 Time taken (s): Real= 0.19, CPU= 0.19, System= 0.00 Min= 0.070 Mean= 0.834 Max= 1.357 DPF> DPF> move 1pgp_lig.pdbqt # small molecule >>> NEW 1,4-interactions will be _ignored_ in the non-bonded internal energy calculation. Ligand PDBQT file = "1pgp_lig.pdbqt" INPUT LIGAND PDBQT FILE: ________________________ INPUT-LIGAND-PDBQT: REMARK 11 active torsions: INPUT-LIGAND-PDBQT: REMARK status: ('A' for Active; 'I' for Inactive) INPUT-LIGAND-PDBQT: REMARK 1 A between atoms: C1_7317 and C2_7318 INPUT-LIGAND-PDBQT: REMARK 2 A between atoms: C4_7322 and O5_7335 INPUT-LIGAND-PDBQT: REMARK 3 A between atoms: O7_7339 and P1_7340 INPUT-LIGAND-PDBQT: REMARK 4 A between atoms: C4_7322 and C5_7324 INPUT-LIGAND-PDBQT: REMARK 5 A between atoms: C3_7320 and C4_7322 INPUT-LIGAND-PDBQT: REMARK 6 A between atoms: C2_7318 and C3_7320 INPUT-LIGAND-PDBQT: REMARK 7 A between atoms: C5_7324 and C6_7326 INPUT-LIGAND-PDBQT: REMARK 8 A between atoms: C2_7318 and O3_7331 INPUT-LIGAND-PDBQT: REMARK 9 A between atoms: C3_7320 and O4_7333 INPUT-LIGAND-PDBQT: REMARK 10 A between atoms: C5_7324 and O6_7337 INPUT-LIGAND-PDBQT: REMARK 11 A between atoms: C6_7326 and O7_7339 INPUT-LIGAND-PDBQT: REMARK RMS_REF 0.6600 INPUT-LIGAND-PDBQT: ROOT INPUT-LIGAND-PDBQT: ATOM 1 C4 PGP 1 22.894 28.598 40.259 1.00 30.80 0.180 C INPUT-LIGAND-PDBQT: ENDROOT INPUT-LIGAND-PDBQT: BRANCH 1 2 INPUT-LIGAND-PDBQT: ATOM 2 C3 PGP 1 21.922 27.809 39.260 1.00 30.93 0.188 C INPUT-LIGAND-PDBQT: BRANCH 2 3 INPUT-LIGAND-PDBQT: ATOM 3 C2 PGP 1 20.328 27.813 39.443 1.00 35.22 0.250 C INPUT-LIGAND-PDBQT: BRANCH 3 4 INPUT-LIGAND-PDBQT: ATOM 4 O3 PGP 1 19.999 27.345 40.750 1.00 40.31 -0.382 OA INPUT-LIGAND-PDBQT: ATOM 5 HO3 PGP 1 19.598 28.087 41.193 1.00 0.00 0.210 HD INPUT-LIGAND-PDBQT: ENDBRANCH 3 4 INPUT-LIGAND-PDBQT: BRANCH 3 6 INPUT-LIGAND-PDBQT: ATOM 6 C1 PGP 1 19.701 29.203 39.198 1.00 35.87 0.205 C INPUT-LIGAND-PDBQT: ATOM 7 O2 PGP 1 18.498 29.386 39.417 1.00 37.45 -0.646 OA INPUT-LIGAND-PDBQT: ATOM 8 O1 PGP 1 20.399 30.200 38.707 1.00 36.75 -0.646 OA INPUT-LIGAND-PDBQT: ENDBRANCH 3 6 INPUT-LIGAND-PDBQT: ENDBRANCH 2 3 INPUT-LIGAND-PDBQT: BRANCH 2 9 INPUT-LIGAND-PDBQT: ATOM 9 O4 PGP 1 22.087 28.265 37.936 1.00 33.78 -0.390 OA INPUT-LIGAND-PDBQT: ATOM 10 HO4 PGP 1 22.065 29.222 38.002 1.00 0.00 0.210 HD INPUT-LIGAND-PDBQT: ENDBRANCH 2 9 INPUT-LIGAND-PDBQT: ENDBRANCH 1 2 INPUT-LIGAND-PDBQT: BRANCH 1 11 INPUT-LIGAND-PDBQT: ATOM 11 O5 PGP 1 22.804 30.023 40.224 1.00 30.90 -0.390 OA INPUT-LIGAND-PDBQT: ATOM 12 HO5 PGP 1 23.534 30.396 40.714 1.00 0.00 0.210 HD INPUT-LIGAND-PDBQT: ENDBRANCH 1 11 INPUT-LIGAND-PDBQT: BRANCH 1 13 INPUT-LIGAND-PDBQT: ATOM 13 C5 PGP 1 24.464 28.252 40.029 1.00 29.83 0.173 C INPUT-LIGAND-PDBQT: BRANCH 13 14 INPUT-LIGAND-PDBQT: ATOM 14 O6 PGP 1 25.163 28.259 41.267 1.00 26.30 -0.391 OA INPUT-LIGAND-PDBQT: ATOM 15 H6 PGP 1 25.947 28.806 41.185 1.00 0.00 0.210 HD INPUT-LIGAND-PDBQT: ENDBRANCH 13 14 INPUT-LIGAND-PDBQT: BRANCH 13 16 INPUT-LIGAND-PDBQT: ATOM 16 C6 PGP 1 25.350 29.132 39.061 1.00 33.11 0.217 C INPUT-LIGAND-PDBQT: BRANCH 16 17 INPUT-LIGAND-PDBQT: ATOM 17 O7 PGP 1 25.797 30.509 39.509 1.00 32.60 -0.405 OA INPUT-LIGAND-PDBQT: BRANCH 17 18 INPUT-LIGAND-PDBQT: ATOM 18 P1 PGP 1 27.362 30.851 39.818 1.00 28.88 0.422 P INPUT-LIGAND-PDBQT: ATOM 19 O8 PGP 1 27.636 30.201 41.167 1.00 30.33 -0.742 OA INPUT-LIGAND-PDBQT: ATOM 20 O9 PGP 1 27.639 32.300 40.093 1.00 26.26 -0.742 OA INPUT-LIGAND-PDBQT: ATOM 21 O10 PGP 1 28.360 30.259 38.733 1.00 30.04 -0.742 OA INPUT-LIGAND-PDBQT: ENDBRANCH 17 18 INPUT-LIGAND-PDBQT: ENDBRANCH 16 17 INPUT-LIGAND-PDBQT: ENDBRANCH 13 16 INPUT-LIGAND-PDBQT: ENDBRANCH 1 13 INPUT-LIGAND-PDBQT: TORSDOF 7 ________________________________________________________________________________ Determining Atom Types and Parameters for the Moving Atoms __________________________________________________________ Number of atoms found in flexible receptor sidechains ("residues") = 0 atoms Total number of atoms found = 21 atoms Number of flexible residues found in the receptor = 0 residues Summary of number of atoms of a given atom type: ------------------------------------------------ Number of atoms with atom type 1 = 6 Number of atoms with atom type 2 = 4 Number of atoms with atom type 3 = 10 Number of atoms with atom type 4 = 1 Summary of total charge on ligand, residues and overall: ------------------------------------------------------- Total charge on ligand = -3.001 e REMARK 11 active torsions: REMARK status: ('A' for Active; 'I' for Inactive) REMARK 1 A between atoms: C1_7317 and C2_7318 REMARK 2 A between atoms: C4_7322 and O5_7335 REMARK 3 A between atoms: O7_7339 and P1_7340 REMARK 4 A between atoms: C4_7322 and C5_7324 REMARK 5 A between atoms: C3_7320 and C4_7322 REMARK 6 A between atoms: C2_7318 and C3_7320 REMARK 7 A between atoms: C5_7324 and C6_7326 REMARK 8 A between atoms: C2_7318 and O3_7331 REMARK 9 A between atoms: C3_7320 and O4_7333 REMARK 10 A between atoms: C5_7324 and O6_7337 REMARK 11 A between atoms: C6_7326 and O7_7339 REMARK RMS_REF 0.6600 TORSDOF record detected: number of torsional degress of freedom has been set to 7. Number of Rotatable Bonds in Small Molecule = 11 torsions TORSION TREE ____________ Sorted in order of increasing number of atoms moved: Torsion # # Atom1--Atom2 Moved List of Atoms Moved ___ ____________ _____ ________________________________________________________ 1 C2--O3 1 HO3. 2 C3--O4 1 HO4. 3 C4--O5 1 HO5. 4 C5--O6 1 H6. 5 C2--C1 2 O2,O1. 6 O7--P1 3 O8,O9,O10. 7 C6--O7 4 P1,O8,O9,O10. 8 C3--C2 5 O3,HO3,C1,O2,O1. 9 C5--C6 5 O7,P1,O8,O9,O10. 10 C4--C3 8 C2,O3,HO3,C1,O2,O1,O4,HO4. 11 C4--C5 8 O6,H6,C6,O7,P1,O8,O9,O10. Matrix of Non-Bonded Interactions: __________________________________ Key: X = non-bonded interaction _ = 1,2 or 1,3 interaction Atom: ID: 1 2 3 4 5 6 7 8 9101112131415161718192021 _____ ___ __________________________________________ C4 1 |_|_|_|_|X|_|X|X|_|_|_|_|_|_|_|_|_|X|X|X|X C3 2 |_|_|_|_|_|_|_|_|_|_|_|_|_|_|X|_|X|X|X|X|X C2 3 |_|_|_|_|_|_|_|_|_|_|_|X|_|X|X|X|X|X|X|X|X O3 4 |_|_|_|_|_|_|_|_|_|X|X|X|X|X|X|X|X|X|X|X|X HO3 5 |X|_|_|_|_|_|X|X|X|X|X|X|X|X|X|X|X|X|X|X|X C1 6 |_|_|_|_|_|_|_|_|_|X|X|X|X|X|X|X|X|X|X|X|X O2 7 |X|_|_|_|X|_|_|_|X|X|X|X|X|X|X|X|X|X|X|X|X O1 8 |X|_|_|_|X|_|_|_|X|X|X|X|X|X|X|X|X|X|X|X|X O4 9 |_|_|_|_|X|_|X|X|_|_|_|X|_|X|X|X|X|X|X|X|X HO4 10 |_|_|_|X|X|X|X|X|_|_|X|X|X|X|X|X|X|X|X|X|X O5 11 |_|_|_|X|X|X|X|X|_|X|_|_|_|_|X|_|X|X|X|X|X HO5 12 |_|_|X|X|X|X|X|X|X|X|_|_|_|X|X|X|X|X|X|X|X C5 13 |_|_|_|X|X|X|X|X|_|X|_|_|_|_|_|_|_|_|X|X|X O6 14 |_|_|X|X|X|X|X|X|X|X|_|X|_|_|_|_|_|X|X|X|X H6 15 |_|X|X|X|X|X|X|X|X|X|X|X|_|_|_|_|X|X|X|X|X C6 16 |_|_|X|X|X|X|X|X|X|X|_|X|_|_|_|_|_|_|_|_|_ O7 17 |_|X|X|X|X|X|X|X|X|X|X|X|_|_|X|_|_|_|_|_|_ P1 18 |X|X|X|X|X|X|X|X|X|X|X|X|_|X|X|_|_|_|_|_|_ O8 19 |X|X|X|X|X|X|X|X|X|X|X|X|X|X|X|_|_|_|_|_|_ O9 20 |X|X|X|X|X|X|X|X|X|X|X|X|X|X|X|_|_|_|_|_|_ O10 21 |X|X|X|X|X|X|X|X|X|X|X|X|X|X|X|_|_|_|_|_|_ List of Internal Non-Bonded Interactions: _________________________________________ First Second Non-Bonded Atom Atom(s) _____ ___________________________________________________ C4: HO3, O2, O1, P1, O8, O9, O10. C3: H6, O7, P1, O8, O9, O10. C2: HO5, O6, H6, C6, O7, P1, O8, O9, O10. O3: HO4, O5, HO5, C5, O6, H6, C6, O7, P1, O8, O9, O10. HO3: O2, O1, O4, HO4, O5, HO5, C5, O6, H6, C6, O7, P1, O8, O9, O10. C1: HO4, O5, HO5, C5, O6, H6, C6, O7, P1, O8, O9, O10. O2: O4, HO4, O5, HO5, C5, O6, H6, C6, O7, P1, O8, O9, O10. O1: O4, HO4, O5, HO5, C5, O6, H6, C6, O7, P1, O8, O9, O10. O4: HO5, O6, H6, C6, O7, P1, O8, O9, O10. HO4: O5, HO5, C5, O6, H6, C6, O7, P1, O8, O9, O10. O5: H6, O7, P1, O8, O9, O10. HO5: O6, H6, C6, O7, P1, O8, O9, O10. C5: O8, O9, O10. O6: P1, O8, O9, O10. H6: O7, P1, O8, O9, O10. Internal Non-bonded Interactions before, 231 and after weeding = 133 Calculating normalized torsion vectors. Number of atoms in ligand: 21 Number of vibrational degrees of freedom of ligand: 57 Number of torsional degrees of freedom = 7 Estimated loss of torsional free energy upon binding = +1.9208 kcal/mol Calculating the product of the partial atomic charges, q1*q2, for all 133 non-bonded pairs... -- Scaled q1*q2 means multiplied by both 332.1 (for conversion later on to kcal/mol) and by the AD4 FF electrostatics coefficient, 0.1465 Non-bonded Scaled Pair Atom1-Atom2 q1*q2 q1*q2 __________ ___________ _________ _________ 1 1-5 0.04 1.84 2 1-7 -0.12 -5.66 3 1-8 -0.12 -5.66 4 1-18 0.08 3.70 5 1-19 -0.13 -6.50 6 1-20 -0.13 -6.50 7 1-21 -0.13 -6.50 8 2-15 0.04 1.92 9 2-17 -0.08 -3.70 10 2-18 0.08 3.86 11 2-19 -0.14 -6.79 12 2-20 -0.14 -6.79 13 2-21 -0.14 -6.79 14 3-12 0.05 2.55 15 3-14 -0.10 -4.76 16 3-15 0.05 2.55 17 3-16 0.05 2.64 18 3-17 -0.10 -4.93 19 3-18 0.11 5.13 20 3-19 -0.19 -9.02 21 3-20 -0.19 -9.02 22 3-21 -0.19 -9.02 23 4-10 -0.08 -3.90 24 4-11 0.15 7.25 25 4-12 -0.08 -3.90 26 4-13 -0.07 -3.21 27 4-14 0.15 7.27 28 4-15 -0.08 -3.90 29 4-16 -0.08 -4.03 30 4-17 0.15 7.53 31 4-18 -0.16 -7.84 32 4-19 0.28 13.79 33 4-20 0.28 13.79 34 4-21 0.28 13.79 35 5-7 -0.14 -6.60 36 5-8 -0.14 -6.60 37 5-9 -0.08 -3.98 38 5-10 0.04 2.15 39 5-11 -0.08 -3.98 40 5-12 0.04 2.15 41 5-13 0.04 1.77 42 5-14 -0.08 -3.99 43 5-15 0.04 2.15 44 5-16 0.05 2.22 45 5-17 -0.09 -4.14 46 5-18 0.09 4.31 47 5-19 -0.16 -7.58 48 5-20 -0.16 -7.58 49 5-21 -0.16 -7.58 50 6-10 0.04 2.09 51 6-11 -0.08 -3.89 52 6-12 0.04 2.09 53 6-13 0.04 1.73 54 6-14 -0.08 -3.90 55 6-15 0.04 2.09 56 6-16 0.04 2.16 57 6-17 -0.08 -4.04 58 6-18 0.09 4.21 59 6-19 -0.15 -7.40 60 6-20 -0.15 -7.40 61 6-21 -0.15 -7.40 62 7-9 0.25 12.26 63 7-10 -0.14 -6.60 64 7-11 0.25 12.26 65 7-12 -0.14 -6.60 66 7-13 -0.11 -5.44 67 7-14 0.25 12.29 68 7-15 -0.14 -6.60 69 7-16 -0.14 -6.82 70 7-17 0.26 12.73 71 7-18 -0.27 -13.26 72 7-19 0.48 23.32 73 7-20 0.48 23.32 74 7-21 0.48 23.32 75 8-9 0.25 12.26 76 8-10 -0.14 -6.60 77 8-11 0.25 12.26 78 8-12 -0.14 -6.60 79 8-13 -0.11 -5.44 80 8-14 0.25 12.29 81 8-15 -0.14 -6.60 82 8-16 -0.14 -6.82 83 8-17 0.26 12.73 84 8-18 -0.27 -13.26 85 8-19 0.48 23.32 86 8-20 0.48 23.32 87 8-21 0.48 23.32 88 9-12 -0.08 -3.98 89 9-14 0.15 7.42 90 9-15 -0.08 -3.98 91 9-16 -0.08 -4.12 92 9-17 0.16 7.68 93 9-18 -0.16 -8.01 94 9-19 0.29 14.08 95 9-20 0.29 14.08 96 9-21 0.29 14.08 97 10-11 -0.08 -3.98 98 10-12 0.04 2.15 99 10-13 0.04 1.77 100 10-14 -0.08 -3.99 101 10-15 0.04 2.15 102 10-16 0.05 2.22 103 10-17 -0.09 -4.14 104 10-18 0.09 4.31 105 10-19 -0.16 -7.58 106 10-20 -0.16 -7.58 107 10-21 -0.16 -7.58 108 11-15 -0.08 -3.98 109 11-17 0.16 7.68 110 11-18 -0.16 -8.01 111 11-19 0.29 14.08 112 11-20 0.29 14.08 113 11-21 0.29 14.08 114 12-14 -0.08 -3.99 115 12-15 0.04 2.15 116 12-16 0.05 2.22 117 12-17 -0.09 -4.14 118 12-18 0.09 4.31 119 12-19 -0.16 -7.58 120 12-20 -0.16 -7.58 121 12-21 -0.16 -7.58 122 13-19 -0.13 -6.24 123 13-20 -0.13 -6.24 124 13-21 -0.13 -6.24 125 14-18 -0.17 -8.03 126 14-19 0.29 14.11 127 14-20 0.29 14.11 128 14-21 0.29 14.11 129 15-17 -0.09 -4.14 130 15-18 0.09 4.31 131 15-19 -0.16 -7.58 132 15-20 -0.16 -7.58 133 15-21 -0.16 -7.58 DPF> about 22.894 28.598 40.259 # small molecule center Small molecule center of rotation = (+22.894, +28.598, +40.259) Translating small molecule by: (-22.894, -28.598, -40.259) Furthest ligand atom from "about" center is 6.021 Angstroms (maxrad). DPF> tran0 22.894 28.598 40.259 # small molecule center Initial translation = (22.894, 28.598, 40.259) Angstroms DPF> quat0 1 0 0 0 # initial quaternion Initial axis-angle, (nx,ny,nz,ang) = ( 1.000, 0.000, 0.000, 0.0 deg ), Normalized axis, (nx,ny,nz) = ( 1.000 0.000 0.000 ) DPF> ndihe 11 # number of active torsions ./bin/autodock4: WARNING! The "ndihe" command is no longer supported. The number of torsions in the PDBQT file(s) is the number that will be used (i.e. 11) DPF> dihe0 0 0 0 0 0 0 0 0 0 0 0 # initial dihedrals (relative) or random 11 initial torsion angles were detected on input line. Initial torsion 1 = 0.00 deg Initial torsion 2 = 0.00 deg Initial torsion 3 = 0.00 deg Initial torsion 4 = 0.00 deg Initial torsion 5 = 0.00 deg Initial torsion 6 = 0.00 deg Initial torsion 7 = 0.00 deg Initial torsion 8 = 0.00 deg Initial torsion 9 = 0.00 deg Initial torsion 10 = 0.00 deg Initial torsion 11 = 0.00 deg DPF> tstep 0.0 # translation step/A Initial cycle, maximum translation step = +/- 0.0 Angstroms DPF> qstep 0.0 # quaternion step/deg Initial cycle, maximum quaternion angle step = +/- 0.0 deg DPF> dstep 0.0 # torsion step/deg Initial cycle, maximum torsion angle step = +/- 0.0 deg DPF> unbound 0.0 # free energy of the unbound state The internal energy of the unbound state was set to +0.000 kcal/mol DPF> DPF> rmstol 2.0 # cluster_tolerance/A Maximum RMS tolerance for conformational cluster analysis = 2.00 Angstroms DPF> epdb 1pgp_lig.pdbqt # >>> NEW WARNING This command, "epdb", currently computes the energy of the ligand specified by the "move lig.pdbqt" command. WARNING -- it will not read in the PDBQT file specified on the "epdb" command line. Number of "true" ligand atoms: 21 Ligand Intramolecular Energy Analysis ===================================== Non-bond Atom1-Atom2 Distance Total Elec vdW+Hb Desolv Sol_fn Type Dielectric ________ ___________ ________ ______ ________ ________ ________ ________ ____ __________ 1 1-5 3.46 +0.035 +0.034 -0.006 +0.007 +0.073 1 15.506 2 1-7 4.54 -0.060 -0.057 -0.012 +0.009 +0.052 1 21.866 3 1-8 3.35 -0.120 -0.114 -0.019 +0.012 +0.075 1 14.881 4 1-18 5.02 +0.022 +0.030 -0.014 +0.006 +0.044 1 24.926 5 1-19 5.09 -0.048 -0.050 -0.006 +0.008 +0.043 1 25.349 6 1-20 6.02 -0.031 -0.034 -0.002 +0.006 +0.029 1 31.581 7 1-21 5.91 -0.032 -0.036 -0.003 +0.006 +0.030 1 30.850 8 2-15 4.57 +0.023 +0.019 -0.001 +0.005 +0.052 1 22.038 9 2-17 4.73 -0.040 -0.034 -0.010 +0.004 +0.049 1 23.033 10 2-18 6.26 +0.018 +0.019 -0.004 +0.004 +0.026 1 33.216 11 2-19 6.48 -0.027 -0.030 -0.002 +0.005 +0.023 1 34.746 12 2-20 7.32 -0.021 -0.023 -0.001 +0.003 +0.015 1 40.446 13 2-21 6.91 -0.023 -0.026 -0.001 +0.004 +0.018 1 37.671 14 3-12 4.31 +0.033 +0.029 -0.002 +0.005 +0.057 1 20.429 15 3-14 5.19 -0.038 -0.035 -0.006 +0.003 +0.041 1 25.986 16 3-15 5.97 +0.016 +0.014 -0.000 +0.003 +0.029 1 31.226 17 3-16 5.21 +0.014 +0.019 -0.009 +0.003 +0.041 1 26.124 18 3-17 6.10 -0.025 -0.025 -0.002 +0.002 +0.028 1 32.109 19 3-18 7.67 +0.016 +0.016 -0.001 +0.002 +0.012 1 42.817 20 3-19 7.88 -0.024 -0.026 -0.000 +0.002 +0.011 1 44.181 21 3-20 8.60 -0.022 -0.022 +0.000 +0.000 +0.010 1 48.790 22 3-21 8.43 -0.022 -0.022 +0.000 +0.000 +0.010 1 47.695 23 4-10 3.92 -0.054 -0.055 -0.002 +0.003 +0.064 1 18.072 24 4-11 3.91 +0.090 +0.102 -0.016 +0.004 +0.064 1 18.072 25 4-12 4.67 -0.035 -0.037 -0.000 +0.002 +0.050 1 22.654 26 4-13 4.61 -0.039 -0.031 -0.011 +0.003 +0.051 1 22.294 27 4-14 5.27 +0.051 +0.052 -0.003 +0.002 +0.040 1 26.537 28 4-15 6.14 -0.018 -0.020 -0.000 +0.001 +0.027 1 32.406 29 4-16 5.89 -0.023 -0.022 -0.003 +0.002 +0.030 1 30.689 30 4-17 6.72 +0.031 +0.031 -0.001 +0.001 +0.020 1 36.385 31 4-18 8.21 -0.021 -0.021 +0.000 +0.000 +0.010 1 46.305 32 4-19 8.16 +0.037 +0.037 +0.000 +0.000 +0.010 1 46.024 33 4-20 9.13 +0.029 +0.029 +0.000 +0.000 +0.010 1 51.944 34 4-21 9.08 +0.029 +0.029 +0.000 +0.000 +0.010 1 51.654 35 5-7 2.46 -0.366 -0.258 -0.113 +0.004 +0.092 1 10.401 36 5-8 3.36 -0.135 -0.131 -0.007 +0.004 +0.075 1 14.956 37 5-9 4.10 -0.049 -0.051 -0.001 +0.003 +0.061 1 19.175 38 5-10 4.19 +0.026 +0.026 -0.000 +0.000 +0.059 1 19.694 39 5-11 3.87 -0.057 -0.058 -0.002 +0.003 +0.065 1 17.792 40 5-12 4.59 +0.021 +0.021 -0.000 +0.000 +0.051 1 22.144 41 5-13 5.01 +0.018 +0.014 -0.001 +0.004 +0.044 1 24.805 42 5-14 5.57 -0.024 -0.025 -0.000 +0.002 +0.035 1 28.533 43 5-15 6.39 +0.010 +0.010 -0.000 +0.000 +0.024 1 34.113 44 5-16 6.22 +0.013 +0.011 -0.000 +0.002 +0.026 1 32.976 45 5-17 6.87 -0.015 -0.016 -0.000 +0.001 +0.019 1 37.376 46 5-18 8.36 +0.011 +0.011 +0.000 +0.000 +0.010 1 47.239 47 5-19 8.31 -0.019 -0.019 +0.000 +0.000 +0.010 1 46.966 48 5-20 9.14 -0.016 -0.016 +0.000 +0.000 +0.010 1 52.023 49 5-21 9.36 -0.015 -0.015 +0.000 +0.000 +0.010 1 53.240 50 6-10 2.65 +0.081 +0.070 +0.002 +0.008 +0.088 1 11.303 51 6-11 3.37 -0.092 -0.077 -0.020 +0.005 +0.075 1 15.006 52 6-12 4.29 +0.028 +0.024 -0.002 +0.005 +0.057 1 20.318 53 6-13 4.93 +0.005 +0.014 -0.012 +0.002 +0.045 1 24.296 54 6-14 5.92 -0.022 -0.021 -0.003 +0.002 +0.030 1 30.886 55 6-15 6.57 +0.011 +0.009 -0.000 +0.002 +0.022 1 35.321 56 6-16 5.65 +0.010 +0.013 -0.006 +0.002 +0.034 1 29.076 57 6-17 6.24 -0.019 -0.020 -0.002 +0.002 +0.026 1 33.096 58 6-18 7.86 +0.013 +0.012 -0.001 +0.002 +0.011 1 44.064 59 6-19 8.24 -0.019 -0.019 +0.000 +0.000 +0.010 1 46.487 60 6-20 8.57 -0.018 -0.018 +0.000 +0.000 +0.010 1 48.565 61 6-21 8.74 -0.017 -0.017 +0.000 +0.000 +0.010 1 49.595 62 7-9 4.04 +0.155 +0.161 -0.014 +0.007 +0.062 1 18.810 63 7-10 3.84 -0.096 -0.097 -0.002 +0.003 +0.066 1 17.652 64 7-11 4.43 +0.129 +0.131 -0.008 +0.006 +0.054 1 21.153 65 7-12 5.30 -0.045 -0.047 -0.000 +0.002 +0.039 1 26.732 66 7-13 6.10 -0.025 -0.028 -0.002 +0.004 +0.028 1 32.162 67 7-14 7.01 +0.047 +0.046 -0.001 +0.002 +0.017 1 38.345 68 7-15 7.68 -0.019 -0.020 -0.000 +0.001 +0.012 1 42.858 69 7-16 6.87 -0.024 -0.027 -0.001 +0.003 +0.019 1 37.376 70 7-17 7.39 +0.043 +0.042 -0.000 +0.002 +0.014 1 40.904 71 7-18 8.99 -0.029 -0.029 +0.000 +0.000 +0.010 1 51.147 72 7-19 9.34 +0.047 +0.047 +0.000 +0.000 +0.010 1 53.146 73 7-20 9.62 +0.044 +0.044 +0.000 +0.000 +0.010 1 54.691 74 7-21 9.92 +0.042 +0.042 +0.000 +0.000 +0.010 1 56.315 75 8-9 2.68 +0.488 +0.398 +0.080 +0.010 +0.088 1 11.474 76 8-10 2.06 -0.754 -0.374 -0.385 +0.005 +0.098 1 8.589 77 8-11 2.85 +0.362 +0.351 +0.002 +0.009 +0.085 1 12.282 78 8-12 3.73 -0.104 -0.104 -0.003 +0.003 +0.068 1 16.989 79 8-13 4.70 -0.053 -0.051 -0.010 +0.008 +0.049 1 22.844 80 8-14 5.75 +0.074 +0.072 -0.002 +0.004 +0.032 1 29.724 81 8-15 6.23 -0.031 -0.032 -0.000 +0.001 +0.026 1 33.045 82 8-16 5.08 -0.052 -0.053 -0.006 +0.007 +0.043 1 25.268 83 8-17 5.47 +0.085 +0.084 -0.002 +0.004 +0.037 1 27.851 84 8-18 7.08 -0.045 -0.048 -0.001 +0.004 +0.017 1 38.843 85 8-19 7.64 +0.073 +0.072 -0.000 +0.002 +0.012 1 42.628 86 8-20 7.66 +0.073 +0.071 -0.000 +0.002 +0.012 1 42.763 87 8-21 7.96 +0.067 +0.065 -0.000 +0.002 +0.010 1 44.722 88 9-12 3.79 -0.060 -0.061 -0.002 +0.003 +0.067 1 17.345 89 9-14 4.53 +0.071 +0.075 -0.007 +0.003 +0.052 1 21.802 90 9-15 5.07 -0.029 -0.031 -0.000 +0.002 +0.043 1 25.248 91 9-16 3.56 -0.094 -0.072 -0.027 +0.005 +0.071 1 16.047 92 9-17 4.61 +0.071 +0.075 -0.007 +0.003 +0.051 1 22.294 93 9-18 6.17 -0.039 -0.040 -0.003 +0.003 +0.027 1 32.597 94 9-19 6.71 +0.060 +0.058 -0.001 +0.003 +0.020 1 36.289 95 9-20 7.19 +0.051 +0.049 -0.000 +0.002 +0.016 1 39.616 96 9-21 6.63 +0.061 +0.059 -0.001 +0.003 +0.021 1 35.759 97 10-11 2.47 -0.255 -0.153 -0.106 +0.004 +0.092 1 10.490 98 10-12 3.30 +0.044 +0.044 -0.000 +0.000 +0.076 1 14.628 99 10-13 3.29 +0.037 +0.037 -0.007 +0.007 +0.076 1 14.551 100 10-14 4.60 -0.037 -0.039 -0.000 +0.002 +0.051 1 22.230 101 10-15 5.04 +0.017 +0.017 -0.000 +0.000 +0.044 1 25.007 102 10-16 3.45 +0.043 +0.042 -0.006 +0.007 +0.073 1 15.456 103 10-17 4.23 -0.047 -0.049 -0.001 +0.003 +0.058 1 19.918 104 10-18 5.83 +0.027 +0.024 -0.000 +0.003 +0.031 1 30.309 105 10-19 6.48 -0.033 -0.034 -0.000 +0.001 +0.023 1 34.746 106 10-20 6.70 -0.030 -0.031 -0.000 +0.001 +0.020 1 36.257 107 10-21 6.42 -0.033 -0.034 -0.000 +0.001 +0.024 1 34.331 108 11-15 3.50 -0.074 -0.072 -0.005 +0.003 +0.072 1 15.753 109 11-17 3.12 +0.156 +0.181 -0.030 +0.005 +0.080 1 13.648 110 11-18 4.65 -0.084 -0.076 -0.014 +0.006 +0.050 1 22.548 111 11-19 4.93 +0.119 +0.118 -0.005 +0.006 +0.045 1 24.296 112 11-20 5.35 +0.099 +0.097 -0.003 +0.005 +0.039 1 27.043 113 11-21 5.76 +0.084 +0.082 -0.002 +0.004 +0.032 1 29.797 114 12-14 2.74 -0.165 -0.124 -0.045 +0.004 +0.087 1 11.755 115 12-15 2.93 +0.057 +0.058 -0.001 +0.000 +0.083 1 12.691 116 12-16 2.76 +0.071 +0.068 -0.005 +0.008 +0.086 1 11.867 117 12-17 2.57 -0.224 -0.148 -0.080 +0.004 +0.090 1 10.900 118 12-18 3.96 +0.062 +0.059 -0.004 +0.007 +0.063 1 18.327 119 12-19 4.13 -0.093 -0.095 -0.001 +0.003 +0.060 1 19.356 120 12-20 4.57 -0.073 -0.075 -0.000 +0.003 +0.052 1 22.016 121 12-21 5.22 -0.054 -0.055 -0.000 +0.002 +0.041 1 26.203 122 13-19 3.89 -0.100 -0.090 -0.023 +0.013 +0.065 1 17.932 123 13-20 5.14 -0.045 -0.047 -0.006 +0.008 +0.042 1 25.728 124 13-21 4.57 -0.063 -0.062 -0.011 +0.010 +0.052 1 22.038 125 14-18 3.70 -0.152 -0.129 -0.031 +0.009 +0.069 1 16.797 126 14-19 3.15 +0.305 +0.325 -0.031 +0.010 +0.079 1 13.805 127 14-20 4.88 +0.122 +0.120 -0.005 +0.006 +0.046 1 24.009 128 14-21 4.54 +0.142 +0.142 -0.007 +0.007 +0.052 1 21.866 129 15-17 2.39 -0.306 -0.171 -0.139 +0.004 +0.093 1 10.101 130 15-18 2.84 +0.129 +0.124 -0.005 +0.009 +0.085 1 12.227 131 15-19 2.19 -0.639 -0.378 -0.266 +0.005 +0.096 1 9.172 132 15-20 4.03 -0.099 -0.100 -0.001 +0.003 +0.062 1 18.765 133 15-21 3.73 -0.119 -0.119 -0.003 +0.003 +0.068 1 17.036 ________ ________ ________ ________ Total -1.582 -0.502 -1.549 +0.469 ________ ________ ________ ________ Total Elec vdW+Hb Desolv Total Intramolecular Interaction Energy = -1.582 kcal/mol Intermolecular Energy Analysis ============================== Atom vdW+Hb+Elec vdW+Hbond Electrosta Partial Coordinates Type Energy Energy tic Energy Charge x y z ____ __________ __________ __________ _______ ________ ________ ________ 1 -0.09 -0.15 0.06 0.180 22.8940 28.5980 40.2590 1 -0.06 -0.21 0.15 0.188 21.9220 27.8090 39.2600 1 -0.01 -0.23 0.22 0.250 20.3280 27.8130 39.4430 3 -0.28 -0.10 -0.19 -0.382 19.9990 27.3450 40.7500 2 0.19 0.11 0.08 0.210 19.5980 28.0870 41.1930 1 -0.27 -0.37 0.10 0.205 19.7010 29.2030 39.1980 3 -0.75 -0.34 -0.41 -0.646 18.4980 29.3860 39.4170 3 0.03 -0.02 0.05 -0.646 20.3990 30.2000 38.7070 3 -1.37 -0.84 -0.53 -0.390 22.0870 28.2650 37.9360 2 0.14 0.03 0.11 0.210 22.0650 29.2220 38.0020 3 -0.14 -0.14 0.00 -0.390 22.8040 30.0230 40.2240 2 0.13 0.12 0.02 0.210 23.5340 30.3960 40.7140 1 -0.09 -0.17 0.08 0.173 24.4640 28.2520 40.0290 3 -0.31 -0.10 -0.22 -0.391 25.1630 28.2590 41.2670 2 0.22 0.10 0.13 0.210 25.9470 28.8060 41.1850 1 -0.14 -0.22 0.08 0.217 25.3500 29.1320 39.0610 3 -0.21 -0.11 -0.10 -0.405 25.7970 30.5090 39.5090 4 0.03 -0.33 0.36 0.422 27.3620 30.8510 39.8180 3 -0.55 0.44 -0.99 -0.742 27.6360 30.2010 41.1670 3 -1.78 -0.57 -1.21 -0.742 27.6390 32.3000 40.0930 3 -0.85 -0.35 -0.50 -0.742 28.3600 30.2590 38.7330 __________ __________ __________ _______ Total -6.17 -3.45 -2.72 -3.001 __________ __________ __________ _______ vdW+Hb+Elec vdW+Hbond Electrosta Partial Energy Energy tic Energy Charge Total Intermolecular Interaction Energy = -7.754 kcal/mol Total Intermolecular vdW + Hbond Energy = -3.454 kcal/mol Total Intermolecular Electrostatic Energy = -2.717 kcal/mol epdb: USER Estimated Free Energy of Binding = -5.83 kcal/mol [=(1)+(2)+(3)-(4)] epdb: USER Estimated Inhibition Constant, Ki = 53.03 uM (micromolar) [Temperature = 298.15 K] epdb: USER epdb: USER (1) Final Intermolecular Energy = -6.17 kcal/mol epdb: USER vdW + Hbond + desolv Energy = -3.45 kcal/mol epdb: USER Electrostatic Energy = -2.72 kcal/mol epdb: USER (2) Final Total Internal Energy = -1.58 kcal/mol epdb: USER (3) Torsional Free Energy = +1.92 kcal/mol epdb: USER (4) Unbound System's Energy = +0.00 kcal/mol epdb: USER epdb: USER DPF> DPF> extnrg 1000.0 # external grid energy External grid energy (beyond grid map walls) = 1000.00 DPF> e0max 0.0 10000 # max initial ernergy; max number of retries Using user-specified maximum number of retries for initialization, 10000 retries. If the initial energy is greater than e0max, 0.000, then a new, random initial state will be created. DPF> DPF> ga_pop_size 150 # number of individuals in population A population of 150 individuals will be used DPF> ga_num_evals 250 # maximum number of energy evaluations There will be at most 250 function evaluations used. DPF> ga_num_generations 4 # maximum number of generations The GA will run for at most 4 generations. DPF> ga_elitism 1 # number of top individuals to survive to next generation The 1 best will be preserved each generation. DPF> ga_mutation_rate 0.02 # rate of gene mutation The mutation rate is 0.020000. DPF> ga_crossover_rate 0.8 # rate of crossover The crossover rate is 0.800000. DPF> ga_window_size 10 # The GA's selection window is 10 generations. DPF> ga_cauchy_alpha 0.0 # Alpha parameter of Cauchy distribution The alpha parameter (for the Cauchy distribution) is being set to 0.000000. DPF> ga_cauchy_beta 1.0 # Beta parameter Cauchy distribution The beta parameter (for the Cauchy distribution) is being set to 1.000000. DPF> set_ga # set the above parameters for GA or LGA DPF> DPF> sw_max_its 30 # iterations of Solis & Wets local search Solis & Wets algorithms will perform at most 30 iterations. DPF> sw_max_succ 2 # consecutive successes before changing rho Solis & Wets algorithms expand rho every 2 in a row successes. DPF> sw_max_fail 2 # consecutive failures before changing rho Solis & Wets algorithms contract rho every 2 in a row failures. DPF> sw_rho 1.0 # size of local search space to sample rho is set to 1.000000. DPF> sw_lb_rho 0.01 # lower bound on rho rho will never get smaller than 0.010000. DPF> ls_search_freq 0.06 # probability of performing local search on individual Local search will be performed with frequency 0.060000. DPF> set_psw1 # set the above pseudo-Solis & Wets parameters Creating a new Local Search object using the pseudo-Solis-Wets algorithm (pSW1) with the current settings. DPF> DPF> ga_run 1 # do this many hybrid GA-LS runs Number of requested LGA dockings = 1 run BEGINNING LAMARCKIAN GENETIC ALGORITHM DOCKING Run: 1 / 1 Date: Sun Feb 22 23:01:04 1970 Output level is set to 0. Creating an initial population of 150 individuals. Assigning a random translation, a random orientation and 11 random torsions to each of the 150 individuals. Beginning Lamarckian Genetic Algorithm (LGA), with a maximum of 250 energy evaluations. Final-Value: -7.754 Run completed; time taken for this run: Real= 0.10s, CPU= 0.10s, System= -0.00s 11:01 04" p.m., 02/22/1970 Total number of Energy Evaluations: 643 Total number of Generations: 1 FINAL LAMARCKIAN GENETIC ALGORITHM DOCKED STATE _______________________________________________ State: 22.894 28.598 40.259 1.000 0.000 0.000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 DOCKED: MODEL 1 DOCKED: USER Run = 1 DOCKED: USER DPF = ./1pgp.dpf DOCKED: USER DOCKED: USER Estimated Free Energy of Binding = -5.83 kcal/mol [=(1)+(2)+(3)-(4)] DOCKED: USER Estimated Inhibition Constant, Ki = 53.03 uM (micromolar) [Temperature = 298.15 K] DOCKED: USER DOCKED: USER (1) Final Intermolecular Energy = -6.17 kcal/mol DOCKED: USER vdW + Hbond + desolv Energy = -3.45 kcal/mol DOCKED: USER Electrostatic Energy = -2.72 kcal/mol DOCKED: USER (2) Final Total Internal Energy = -1.58 kcal/mol DOCKED: USER (3) Torsional Free Energy = +1.92 kcal/mol DOCKED: USER (4) Unbound System's Energy = +0.00 kcal/mol DOCKED: USER DOCKED: USER DOCKED: USER NEWDPF move 1pgp_lig.pdbqt DOCKED: USER NEWDPF about 22.893999 28.598000 40.258999 DOCKED: USER NEWDPF tran0 22.894000 28.598000 40.259000 DOCKED: USER NEWDPF quaternion0 0.000000 0.000000 0.000000 1.000000 DOCKED: USER NEWDPF axisangle0 1.000000 0.000000 0.000000 0.000000 DOCKED: USER NEWDPF quat0 1.000000 0.000000 0.000000 0.000000 # deprecated DOCKED: USER NEWDPF dihe0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 DOCKED: USER DOCKED: REMARK 11 active torsions: DOCKED: REMARK status: ('A' for Active; 'I' for Inactive) DOCKED: REMARK 1 A between atoms: C1_7317 and C2_7318 DOCKED: REMARK 2 A between atoms: C4_7322 and O5_7335 DOCKED: REMARK 3 A between atoms: O7_7339 and P1_7340 DOCKED: REMARK 4 A between atoms: C4_7322 and C5_7324 DOCKED: REMARK 5 A between atoms: C3_7320 and C4_7322 DOCKED: REMARK 6 A between atoms: C2_7318 and C3_7320 DOCKED: REMARK 7 A between atoms: C5_7324 and C6_7326 DOCKED: REMARK 8 A between atoms: C2_7318 and O3_7331 DOCKED: REMARK 9 A between atoms: C3_7320 and O4_7333 DOCKED: REMARK 10 A between atoms: C5_7324 and O6_7337 DOCKED: REMARK 11 A between atoms: C6_7326 and O7_7339 DOCKED: REMARK RMS_REF 0.6600 DOCKED: USER x y z vdW Elec q Type DOCKED: USER _______ _______ _______ _____ _____ ______ ____ DOCKED: ROOT DOCKED: ATOM 1 C4 PGP 1 22.894 28.598 40.259 -0.15 +0.06 +0.180 C DOCKED: ENDROOT DOCKED: BRANCH 1 2 DOCKED: ATOM 2 C3 PGP 1 21.922 27.809 39.260 -0.21 +0.15 +0.188 C DOCKED: BRANCH 2 3 DOCKED: ATOM 3 C2 PGP 1 20.328 27.813 39.443 -0.23 +0.22 +0.250 C DOCKED: BRANCH 3 4 DOCKED: ATOM 4 O3 PGP 1 19.999 27.345 40.750 -0.10 -0.19 -0.382 OA DOCKED: ATOM 5 HO3 PGP 1 19.598 28.087 41.193 +0.11 +0.08 +0.210 HD DOCKED: ENDBRANCH 3 4 DOCKED: BRANCH 3 6 DOCKED: ATOM 6 C1 PGP 1 19.701 29.203 39.198 -0.37 +0.10 +0.205 C DOCKED: ATOM 7 O2 PGP 1 18.498 29.386 39.417 -0.34 -0.41 -0.646 OA DOCKED: ATOM 8 O1 PGP 1 20.399 30.200 38.707 -0.02 +0.05 -0.646 OA DOCKED: ENDBRANCH 3 6 DOCKED: ENDBRANCH 2 3 DOCKED: BRANCH 2 9 DOCKED: ATOM 9 O4 PGP 1 22.087 28.265 37.936 -0.84 -0.53 -0.390 OA DOCKED: ATOM 10 HO4 PGP 1 22.065 29.222 38.002 +0.03 +0.11 +0.210 HD DOCKED: ENDBRANCH 2 9 DOCKED: ENDBRANCH 1 2 DOCKED: BRANCH 1 11 DOCKED: ATOM 11 O5 PGP 1 22.804 30.023 40.224 -0.14 +0.00 -0.390 OA DOCKED: ATOM 12 HO5 PGP 1 23.534 30.396 40.714 +0.12 +0.02 +0.210 HD DOCKED: ENDBRANCH 1 11 DOCKED: BRANCH 1 13 DOCKED: ATOM 13 C5 PGP 1 24.464 28.252 40.029 -0.17 +0.08 +0.173 C DOCKED: BRANCH 13 14 DOCKED: ATOM 14 O6 PGP 1 25.163 28.259 41.267 -0.10 -0.22 -0.391 OA DOCKED: ATOM 15 H6 PGP 1 25.947 28.806 41.185 +0.10 +0.13 +0.210 HD DOCKED: ENDBRANCH 13 14 DOCKED: BRANCH 13 16 DOCKED: ATOM 16 C6 PGP 1 25.350 29.132 39.061 -0.22 +0.08 +0.217 C DOCKED: BRANCH 16 17 DOCKED: ATOM 17 O7 PGP 1 25.797 30.509 39.509 -0.11 -0.10 -0.405 OA DOCKED: BRANCH 17 18 DOCKED: ATOM 18 P1 PGP 1 27.362 30.851 39.818 -0.33 +0.36 +0.422 P DOCKED: ATOM 19 O8 PGP 1 27.636 30.201 41.167 +0.44 -0.99 -0.742 OA DOCKED: ATOM 20 O9 PGP 1 27.639 32.300 40.093 -0.57 -1.21 -0.742 OA DOCKED: ATOM 21 O10 PGP 1 28.360 30.259 38.733 -0.35 -0.50 -0.742 OA DOCKED: ENDBRANCH 17 18 DOCKED: ENDBRANCH 16 17 DOCKED: ENDBRANCH 13 16 DOCKED: ENDBRANCH 1 13 DOCKED: TORSDOF 7 DOCKED: TER DOCKED: ENDMDL ________________________________________________________________________________ DPF> DPF> analysis CLUSTER ANALYSIS OF CONFORMATIONS _________________________________ Number of conformations = 1 RMSD cluster analysis will be performed using the ligand atoms only (21 / 21 total atoms). STATE VARIABLES: ________________ Translation x,y,z = 22.894 28.598 40.259 Quaternion x,y,z,w = 0.000 0.000 0.000 1.000 Axis-Angle nx,ny,nz,angle = 1.000 0.000 0.000 0.000 Number of Torsions = 11 Torsions (degrees) = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 Sorry! Unable to perform cluster analysis, because not enough conformations were generated. MODEL 1 USER Run = 1 USER Cluster Rank = 1 USER Number of conformations in this cluster = 1 USER USER RMSD from reference structure = 54.784 A USER USER Estimated Free Energy of Binding = -5.83 kcal/mol [=(1)+(2)+(3)-(4)] USER Estimated Inhibition Constant, Ki = 53.03 uM (micromolar) [Temperature = 298.15 K] USER USER (1) Final Intermolecular Energy = -6.17 kcal/mol USER vdW + Hbond + desolv Energy = -3.45 kcal/mol USER Electrostatic Energy = -2.72 kcal/mol USER (2) Final Total Internal Energy = -1.58 kcal/mol USER (3) Torsional Free Energy = +1.92 kcal/mol USER (4) Unbound System's Energy = +0.00 kcal/mol USER USER USER USER DPF = ./1pgp.dpf USER NEWDPF move 1pgp_lig.pdbqt USER NEWDPF about 22.893999 28.598000 40.258999 USER NEWDPF tran0 22.894000 28.598000 40.259000 USER NEWDPF axisangle0 1.000000 0.000000 0.000000 0.000000 USER NEWDPF quaternion0 0.000000 0.000000 0.000000 1.000000 USER NEWDPF ndihe 11 USER NEWDPF dihe0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 USER USER x y z vdW Elec q RMS ATOM 1 C4 PGP 1 22.894 28.598 40.259 -0.15 +0.06 +0.180 54.784 ATOM 2 C3 PGP 1 21.922 27.809 39.260 -0.21 +0.15 +0.188 54.784 ATOM 3 C2 PGP 1 20.328 27.813 39.443 -0.23 +0.22 +0.250 54.784 ATOM 4 O3 PGP 1 19.999 27.345 40.750 -0.10 -0.19 -0.382 54.784 ATOM 5 HO3 PGP 1 19.598 28.087 41.193 +0.11 +0.08 +0.210 54.784 ATOM 6 C1 PGP 1 19.701 29.203 39.198 -0.37 +0.10 +0.205 54.784 ATOM 7 O2 PGP 1 18.498 29.386 39.417 -0.34 -0.41 -0.646 54.784 ATOM 8 O1 PGP 1 20.399 30.200 38.707 -0.02 +0.05 -0.646 54.784 ATOM 9 O4 PGP 1 22.087 28.265 37.936 -0.84 -0.53 -0.390 54.784 ATOM 10 HO4 PGP 1 22.065 29.222 38.002 +0.03 +0.11 +0.210 54.784 ATOM 11 O5 PGP 1 22.804 30.023 40.224 -0.14 +0.00 -0.390 54.784 ATOM 12 HO5 PGP 1 23.534 30.396 40.714 +0.12 +0.02 +0.210 54.784 ATOM 13 C5 PGP 1 24.464 28.252 40.029 -0.17 +0.08 +0.173 54.784 ATOM 14 O6 PGP 1 25.163 28.259 41.267 -0.10 -0.22 -0.391 54.784 ATOM 15 H6 PGP 1 25.947 28.806 41.185 +0.10 +0.13 +0.210 54.784 ATOM 16 C6 PGP 1 25.350 29.132 39.061 -0.22 +0.08 +0.217 54.784 ATOM 17 O7 PGP 1 25.797 30.509 39.509 -0.11 -0.10 -0.405 54.784 ATOM 18 P1 PGP 1 27.362 30.851 39.818 -0.33 +0.36 +0.422 54.784 ATOM 19 O8 PGP 1 27.636 30.201 41.167 +0.44 -0.99 -0.742 54.784 ATOM 20 O9 PGP 1 27.639 32.300 40.093 -0.57 -1.21 -0.742 54.784 ATOM 21 O10 PGP 1 28.360 30.259 38.733 -0.35 -0.50 -0.742 54.784 TER ENDMDL AVSFLD: # AVS field file AVSFLD: # AVSFLD: # Created by AutoDock AVSFLD: # AVSFLD: ndim=2 # number of dimensions in the field AVSFLD: nspace=1 # number of physical coordinates AVSFLD: veclen=7 # vector size AVSFLD: dim1=21 # atoms AVSFLD: dim2=1 # conformations AVSFLD: data=Real # data type (byte,integer,Real,double) AVSFLD: field=uniform # field coordinate layout AVSFLD: label= x y z vdW Elec q RMS AVSFLD: variable 1 file = ./1pgp.dlg.pdb filetype = ascii offset = 5 stride = 12 AVSFLD: variable 2 file = ./1pgp.dlg.pdb filetype = ascii offset = 6 stride = 12 AVSFLD: variable 3 file = ./1pgp.dlg.pdb filetype = ascii offset = 7 stride = 12 AVSFLD: variable 4 file = ./1pgp.dlg.pdb filetype = ascii offset = 8 stride = 12 AVSFLD: variable 5 file = ./1pgp.dlg.pdb filetype = ascii offset = 9 stride = 12 AVSFLD: variable 6 file = ./1pgp.dlg.pdb filetype = ascii offset = 10 stride = 12 AVSFLD: variable 7 file = ./1pgp.dlg.pdb filetype = ascii offset = 11 stride = 12 AVSFLD: # end of file >>> Closing the docking parameter file (DPF)... This docking finished at: 11:01 04" p.m., 02/22/1970 ________________________________________________________________________________ ./bin/autodock4: Successful Completion on "mac-90023.lal.in2p3.fr" Real= 1.61s, CPU= 1.44s, System= 0.15s ________________________________________________________________________________