jackygrahamez
07-01-2007, 06:05 PM
I looked at my upload directory and found some of the output consistent with how it runs in standalone, despite the BOINC errors. This is the output for the following result
ad_0701071731_nodelete_14_0
[root@vps c]# cat *14*
__________________________________________________ ______________
__________//___________________________/////___________________/____________
_________/__/__________________________/____/__________________/____________
________/____/___________/_____________/_____/_________________/____________
________/____/__/_____/_/////___/////__/_____/__/////___/////__/___/________
_______/______/_/_____/__/_____/_____/_/_____/_/_____/_/_____/_/_//_________
_______////////_/_____/__/_____/_____/_/_____/_/_____/_/_______//_/_________
_______/______/_/____//__/___/_/_____/_/____/__/_____/_/_____/_/___/________
_______/______/__////_/___///___/////__/////____/////___/////__/____/_______
__________________________________________________ ______________
______
/ \
/ \
/ \
\ /\ /
\ / \ /
\/ /\ \/
/ \
/____\
______________________________________
| |
| 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: 1:43 43" p.m., 07/01/2007
using: "tecra8100"
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: in
DPF> outlev 0
Output Level = 0.
Output every 30000 generations.
DPF> parameter_file AD4_parameters.dat # New parameter library >>> NEW
jackygrahamez
07-01-2007, 06:29 PM
This is a successful run from my desktop
__________________________________________________ ______________
__________//___________________________/////___________________/____________
_________/__/__________________________/____/__________________/____________
________/____/___________/_____________/_____/_________________/____________
________/____/__/_____/_/////___/////__/_____/__/////___/////__/___/________
_______/______/_/_____/__/_____/_____/_/_____/_/_____/_/_____/_/_//_________
_______////////_/_____/__/_____/_____/_/_____/_/_____/_/_______//_/_________
_______/______/_/____//__/___/_/_____/_/____/__/_____/_/_____/_/___/________
_______/______/__////_/___///___/////__/////____/////___/////__/____/_______
__________________________________________________ ______________
______
/ \
/ \
/ \
\ /\ /
\ / \ /
\/ /\ \/
/ \
/____\
______________________________________
| |
| 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: 2:30 03" p.m., 07/01/2007
using: "H-XPJSHULTZ"
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 internal energy calculations:
392586.8 0.0
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 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= 0.02, CPU= 0.02, 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 internal energy calculations:
392586.8 0.0
E = ----------- - -----------
C,HD 12 6
r 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 internal energy calculations:
392586.8 0.0
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 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= 0.00, 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 internal energy calculations:
392586.8 0.0
E = ----------- - -----------
C,P 12 6
r r
Calculating C-P interaction energy versus atomic separation (2048 data points).
Time taken: Real= 0.00, CPU= 0.00, 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= 0.00, 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 internal energy calculations:
392586.8 0.0
E = ----------- - -----------
HD,HD 12 6
r r
Calculating HD-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 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= 0.02, CPU= 0.02, 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 internal energy calculations:
392586.8 0.0
E = ----------- - -----------
HD,OA 12 6
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 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= 0.00, 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 internal energy calculations:
392586.8 0.0
E = ----------- - -----------
HD,P 12 6
r r
Calculating HD-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 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 internal energy calculations:
392586.8 0.0
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 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= 0.00, 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 internal energy calculations:
392586.8 0.0
E = ----------- - -----------
OA,P 12 6
r r
Calculating OA-P interaction energy versus atomic separation (2048 data points).
Time taken: Real= 0.00, CPU= 0.00, 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 internal energy calculations:
392586.8 0.0
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
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= 0.13, CPU= 0.09, System= 0.03
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= 0.14, CPU= 0.13, System= 0.02
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= 0.13, CPU= 0.13, System= 0.00
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= 0.13, CPU= 0.13, 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= 0.11, CPU= 0.09, System= 0.02
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= 0.11, CPU= 0.11, 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
autodock_4.01_windows_intelx86: 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 Jul 1 14:30:04 2007
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= 0.23s, CPU= 0.23s, System= 0.00s
2:30 04" p.m., 07/01/2007
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: 2:30 04" p.m., 07/01/2007
__________________________________________________ ______________________________
autodock_4.01_windows_intelx86: Successful Completion on "H-XPJSHULTZ"
Real= 1.25s, CPU= 1.14s, System= 0.09s
__________________________________________________ ______________________________
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