I'm running PyMOL v-2.2.0a0 on my Debian Stretch Platform and installed
the current autodock plugin.
Execution of the plugin on a test system 1ACL.pdb (I have run this
system with MGL_Tools as the gui) did produce correct results.
However the execution of the plugin differed from what I have seen in
earlier versions of PyMOL.
Also, none of the run messages were displayed in PyMOL during the
execution of autogrid and autodock. I monitored the execution of both
in a text editor.
Also when I attempted loading the docking log in View Poses the only
files that were found were DME.pdbqt for the ligand and
receptor.1acl.pdbqt for the protein.
The PyMOL messages are:
PyMOL(TM) Molecular Graphics System, Version 2.2.0a0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable
scientific
software by purchasing a PyMOL Maintenance and/or Support
subscription.
More information can be found at "http://www.pymol.org";.
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 3.0. Shaders available.
Detected GLSL version 1.30.
OpenGL graphics engine:
GL_VENDOR: nouveau
GL_RENDERER: Gallium 0.4 on NVD9
GL_VERSION: 3.0 Mesa 13.0.6
Detected blacklisted graphics driver. Disabling shaders.
Detected 8 CPU cores. Enabled multithreaded rendering.
HEADER HYDROLASE(CARBOXYLIC ESTERASE) 18-AUG-93 1ACL
TITLE QUATERNARY LIGAND BINDING TO AROMATIC RESIDUES IN THE ACTIVE-SITE
TITLE 2 GORGE OF ACETYLCHOLINESTERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ACETYLCHOLINESTERASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.1.1.7;
COMPND 5 ENGINEERED: YES
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
CmdLoad: PDB-string loaded into object "1acl_m", state 1.
CmdLoad: PDB-string loaded into object "DME", state 1.
/home/comp/Apps/Models/1ACL/PyMOL_Test
/home/comp/Apps/Models/1ACL/PyMOL_Test/receptor.1acl_m.pdb
Exception in thread Thread-3:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File
"/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line
255, in run
self.page.insert('end', "%s" % line)
File "<string>", line 1, in insert
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 3113, in insert
self.tk.call((self._w, 'insert', index, chars) + args)
RuntimeError: main thread is not in main loop
Exception in thread Thread-5:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File
"/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line
255, in run
self.page.insert('end', "%s" % line)
File "<string>", line 1, in insert
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 3113, in insert
self.tk.call((self._w, 'insert', index, chars) + args)
RuntimeError: main thread is not in main loop
<type 'exceptions.AttributeError'> Exception in Tk callback
Function: <bound method Autodock.load_ligand_file of
<pmg_tk.startup.autodock_plugin.Autodock instance at 0x2b26d45ace18>>
(type: <type 'instancemethod'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
return apply(self.func, args)
File
"/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line
2459, in load_ligand_file
self.load_pdbqt(filename)
File
"/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line
2513, in load_pdbqt
lst = self.fileopen(filename, 'r').readlines()
<type 'exceptions.AttributeError'>: 'NoneType' object has no attribute
'readlines'
<type 'exceptions.ValueError'> Exception in Tk callback
Function: <bound method Autodock.load_ligand_file of
<pmg_tk.startup.autodock_plugin.Autodock instance at 0x2b26d45ace18>>
(type: <type 'instancemethod'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
return apply(self.func, args)
File
"/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line
2459, in load_ligand_file
self.load_pdbqt(filename)
File
"/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line
2540, in load_pdbqt
self.update_combo(name)
File
"/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line
2547, in update_combo
self.pose_viewer_ligand_pages[name] = {'name':
self.pose_viewer_notebook.add(name)}
File
"/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwNoteBook.py", line
204, in add
return apply(self.insert, (pageName, len(self._pageNames)), kw)
File
"/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwNoteBook.py", line
153, in insert
Tkinter.Frame, self._hull), pageOptions)
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 465, in createcomponent
'Component name "%s" must not contain "_"' % componentName
<type 'exceptions.ValueError'>: Component name "receptor.1acl_m" must
not contain "_"
The run.log and DME.dlg are also attached.
All very confusing.
Thanks in advance for your comments.
--
Stephen P. Molnar, Ph.D.
Consultant
www.molecular-modeling.net
(614)312-7528 (c)
Skype: smolnar1
Script started on Tue 05 Jun 2018 09:12:18 AM EDT
]0;comp@AbNormal: ~/Apps/Models/1ACL/PyMOL_Test[01;32mcomp@AbNormal[00m:[01;34m~/Apps/Models/1ACL/PyMOL_Test[00m$ /home/comp/Apps/PyMOL/pymol
PyMOL(TM) Molecular Graphics System, Version 2.2.0a0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org";.
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 3.0. Shaders available.
Detected GLSL version 1.30.
OpenGL graphics engine:
GL_VENDOR: nouveau
GL_RENDERER: Gallium 0.4 on NVD9
GL_VERSION: 3.0 Mesa 13.0.6
Detected blacklisted graphics driver. Disabling shaders.
Detected 8 CPU cores. Enabled multithreaded rendering.
Gtk-[1;32mMessage[0m: GtkDialog mapped without a transient parent. This is discouraged.
HEADER HYDROLASE(CARBOXYLIC ESTERASE) 18-AUG-93 1ACL
TITLE QUATERNARY LIGAND BINDING TO AROMATIC RESIDUES IN THE ACTIVE-SITE
TITLE 2 GORGE OF ACETYLCHOLINESTERASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ACETYLCHOLINESTERASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.1.1.7;
COMPND 5 ENGINEERED: YES
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
CmdLoad: PDB-string loaded into object "1acl_m", state 1.
CmdLoad: PDB-string loaded into object "DME", state 1.
/home/comp/Apps/Models/1ACL/PyMOL_Test
/home/comp/Apps/Models/1ACL/PyMOL_Test/receptor.1acl_m.pdb
Exception in thread Thread-3:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 255, in run
self.page.insert('end', "%s" % line)
File "<string>", line 1, in insert
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 3113, in insert
self.tk.call((self._w, 'insert', index, chars) + args)
RuntimeError: main thread is not in main loop
/home/comp/Apps/Autodock/autodock4: WARNING: Using autodock4.0 unbound extended model in autodock4.2!
Exception in thread Thread-5:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 255, in run
self.page.insert('end', "%s" % line)
File "<string>", line 1, in insert
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 3113, in insert
self.tk.call((self._w, 'insert', index, chars) + args)
RuntimeError: main thread is not in main loop
<type 'exceptions.AttributeError'> Exception in Tk callback
Function: <bound method Autodock.load_ligand_file of <pmg_tk.startup.autodock_plugin.Autodock instance at 0x2b26d45ace18>> (type: <type 'instancemethod'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2459, in load_ligand_file
self.load_pdbqt(filename)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2513, in load_pdbqt
lst = self.fileopen(filename, 'r').readlines()
<type 'exceptions.AttributeError'>: 'NoneType' object has no attribute 'readlines'
Gtk-[1;32mMessage[0m: GtkDialog mapped without a transient parent. This is discouraged.
<type 'exceptions.ValueError'> Exception in Tk callback
Function: <bound method Autodock.load_ligand_file of <pmg_tk.startup.autodock_plugin.Autodock instance at 0x2b26d45ace18>> (type: <type 'instancemethod'>)
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2459, in load_ligand_file
self.load_pdbqt(filename)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2540, in load_pdbqt
self.update_combo(name)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2547, in update_combo
self.pose_viewer_ligand_pages[name] = {'name': self.pose_viewer_notebook.add(name)}
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwNoteBook.py", line 204, in add
return apply(self.insert, (pageName, len(self._pageNames)), kw)
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwNoteBook.py", line 153, in insert
Tkinter.Frame, self._hull), pageOptions)
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 465, in createcomponent
'Component name "%s" must not contain "_"' % componentName
<type 'exceptions.ValueError'>: Component name "receptor.1acl_m" must not contain "_"
Gtk-[1;32mMessage[0m: GtkDialog mapped without a transient parent. This is discouraged.
]0;comp@AbNormal: ~/Apps/Models/1ACL/PyMOL_Test[01;32mcomp@AbNormal[00m:[01;34m~/Apps/Models/1ACL/PyMOL_Test[00m$ exit
Script done on Tue 05 Jun 2018 09:23:03 AM EDT
AutoDock 4.2 Release 4.2.6
(C) 1989-2012 The Scripps Research Institute
AutoDock comes with ABSOLUTELY NO WARRANTY.
AutoDock is free software, and you are welcome
to redistribute it under certain conditions;
for details type 'autodock4 -C'
main.cc $Revision: 1.213 $
Compiled on Apr 20 2018 at 08:55:46
This file was created at: 9:17 05" a.m., 06/05/2018
on host: "AbNormal"
Current Working Directory = "/home/comp/Apps/Models/1ACL/PyMOL_Test"
________________________________________________________________
SETTING UP DEFAULT PARAMETER LIBRARY
________________________________________________________________
Random number generator was seeded with values 15560, 1528204625.
Docking parameter file (DPF) used for this docking: DME.dpf
DPF> autodock_parameter_version 4.2 # used by autodock to validate
parameter set
Autodock parameter version 4.2.
DPF> outlev 1 # diagnostic output level
Output Level = 1 ADT-COMPATIBLE OUTPUT DURING DOCKING.
DPF> intelec # calculate internal electrostatics
Electrostatic energies will be calculated for all non-bonds between moving
atoms.
DPF> seed pid time # seeds for random generator
Random number generator was seeded with values 15560, 1528204625.
DPF> ligand_types C N # atoms types in ligand
DPF> fld receptor.1acl_m.maps.fld # grid_data_file
Opening Grid Map Dimensions file: receptor.1acl_m.maps.fld
Grid Point Spacing = 0.375 Angstroms
Even Number of User-specified Grid Points = 60 x-points
60 y-points
60 z-points
Coordinates of Central Grid Point of Maps = (3.140, 65.850, 67.780)
Macromolecule file used to create Grid Maps = receptor.1acl_m.pdbqt
Grid Parameter file used to create Grid Maps = 1acl_m.gpf
Minimum coordinates in grid = (-8.110, 54.600, 56.530)
Maximum coordinates in grid = (14.390, 77.100, 79.030)
DPF> map receptor.1acl_m.C.map # atom-specific affinity map
DPF> map receptor.1acl_m.N.map # atom-specific affinity map
DPF> elecmap receptor.1acl_m.e.map # electrostatics map
DPF> desolvmap receptor.1acl_m.d.map # desolvation map
DPF> move DME.pdbqt # small molecule
1,4-interactions will be _ignored_ in the non-bonded internal energy
calculation.
Ligand PDBQT file = "DME.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: N1_1 and C2_2
INPUT-LIGAND-PDBQT: REMARK 2 A between atoms: C2_2 and C3_3
INPUT-LIGAND-PDBQT: REMARK 3 A between atoms: C3_3 and C4_4
INPUT-LIGAND-PDBQT: REMARK 4 A between atoms: C4_4 and C5_5
INPUT-LIGAND-PDBQT: REMARK 5 A between atoms: C5_5 and C6_6
INPUT-LIGAND-PDBQT: REMARK 6 A between atoms: C6_6 and C7_7
INPUT-LIGAND-PDBQT: REMARK 7 A between atoms: C7_7 and C8_8
INPUT-LIGAND-PDBQT: REMARK 8 A between atoms: C8_8 and C9_9
INPUT-LIGAND-PDBQT: REMARK 9 A between atoms: C9_9 and C10_10
INPUT-LIGAND-PDBQT: REMARK 10 A between atoms: C10_10 and C11_11
INPUT-LIGAND-PDBQT: REMARK 11 A between atoms: C11_11 and N12_12
INPUT-LIGAND-PDBQT: ROOT
INPUT-LIGAND-PDBQT: HETATM 1 C6 DME A 999 5.009 65.507 68.892
1.00 14.60 0.000 C
INPUT-LIGAND-PDBQT: ENDROOT
INPUT-LIGAND-PDBQT: BRANCH 1 2
INPUT-LIGAND-PDBQT: HETATM 2 C5 DME A 999 3.767 65.143 69.695
1.00 20.97 0.000 C
INPUT-LIGAND-PDBQT: BRANCH 2 3
INPUT-LIGAND-PDBQT: HETATM 3 C4 DME A 999 3.211 63.724 69.452
1.00 19.57 0.002 C
INPUT-LIGAND-PDBQT: BRANCH 3 4
INPUT-LIGAND-PDBQT: HETATM 4 C3 DME A 999 1.939 63.625 70.294
1.00 19.23 0.028 C
INPUT-LIGAND-PDBQT: BRANCH 4 5
INPUT-LIGAND-PDBQT: HETATM 5 C2 DME A 999 1.174 62.295 70.340
1.00 20.34 0.236 C
INPUT-LIGAND-PDBQT: BRANCH 5 6
INPUT-LIGAND-PDBQT: HETATM 6 N1 DME A 999 0.354 62.248 71.567
1.00 21.86 -0.079 N
INPUT-LIGAND-PDBQT: HETATM 7 C13 DME A 999 -0.382 63.521 71.796
1.00 24.30 0.271 C
INPUT-LIGAND-PDBQT: HETATM 8 C14 DME A 999 -0.683 61.201 71.454
1.00 24.41 0.271 C
INPUT-LIGAND-PDBQT: HETATM 9 C15 DME A 999 1.203 61.900 72.734
1.00 25.02 0.271 C
INPUT-LIGAND-PDBQT: ENDBRANCH 5 6
INPUT-LIGAND-PDBQT: ENDBRANCH 4 5
INPUT-LIGAND-PDBQT: ENDBRANCH 3 4
INPUT-LIGAND-PDBQT: ENDBRANCH 2 3
INPUT-LIGAND-PDBQT: ENDBRANCH 1 2
INPUT-LIGAND-PDBQT: BRANCH 1 10
INPUT-LIGAND-PDBQT: HETATM 10 C7 DME A 999 4.749 66.485 67.771
1.00 20.98 0.000 C
INPUT-LIGAND-PDBQT: BRANCH 10 11
INPUT-LIGAND-PDBQT: HETATM 11 C8 DME A 999 4.339 67.920 68.136
1.00 12.44 0.000 C
INPUT-LIGAND-PDBQT: BRANCH 11 12
INPUT-LIGAND-PDBQT: HETATM 12 C9 DME A 999 3.711 68.650 66.914
1.00 20.29 0.002 C
INPUT-LIGAND-PDBQT: BRANCH 12 13
INPUT-LIGAND-PDBQT: HETATM 13 C10 DME A 999 4.292 68.241 65.534
1.00 22.74 0.028 C
INPUT-LIGAND-PDBQT: BRANCH 13 14
INPUT-LIGAND-PDBQT: HETATM 14 C11 DME A 999 3.840 69.056 64.293
1.00 26.94 0.236 C
INPUT-LIGAND-PDBQT: BRANCH 14 15
INPUT-LIGAND-PDBQT: HETATM 15 N12 DME A 999 4.766 68.964 63.115
1.00 25.24 -0.079 N
INPUT-LIGAND-PDBQT: HETATM 16 C16 DME A 999 5.964 69.816 63.326
1.00 18.56 0.271 C
INPUT-LIGAND-PDBQT: HETATM 17 C17 DME A 999 4.072 69.378 61.885
1.00 19.07 0.271 C
INPUT-LIGAND-PDBQT: HETATM 18 C18 DME A 999 5.167 67.571 62.883
1.00 28.44 0.271 C
INPUT-LIGAND-PDBQT: ENDBRANCH 14 15
INPUT-LIGAND-PDBQT: ENDBRANCH 13 14
INPUT-LIGAND-PDBQT: ENDBRANCH 12 13
INPUT-LIGAND-PDBQT: ENDBRANCH 11 12
INPUT-LIGAND-PDBQT: ENDBRANCH 10 11
INPUT-LIGAND-PDBQT: ENDBRANCH 1 10
INPUT-LIGAND-PDBQT: TORSDOF 11
________________________________________________________________________________
Total charge on ligand = +2.000 e
REMARK 11 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: N1_1 and C2_2
REMARK 2 A between atoms: C2_2 and C3_3
REMARK 3 A between atoms: C3_3 and C4_4
REMARK 4 A between atoms: C4_4 and C5_5
REMARK 5 A between atoms: C5_5 and C6_6
REMARK 6 A between atoms: C6_6 and C7_7
REMARK 7 A between atoms: C7_7 and C8_8
REMARK 8 A between atoms: C8_8 and C9_9
REMARK 9 A between atoms: C9_9 and C10_10
REMARK 10 A between atoms: C10_10 and C11_11
REMARK 11 A between atoms: C11_11 and N12_12
Number of Rotatable Bonds in Small Molecule = 11 torsions
Number of atoms in ligand: 18
Number of non-hydrogen atoms in ligand: 18
Number of vibrational degrees of freedom of ligand: 48
Number of torsional degrees of freedom = 11
Estimated loss of torsional free energy upon binding = +3.2813 kcal/mol
DPF> about 3.1384 65.8469 67.7823 # small molecule center
Small molecule center of rotation = (+3.138, +65.847, +67.782)
DPF> tran0 random # initial coordinates/A or random
Initial translation = (10.166, 62.616, 75.748) Angstroms
DPF> quaternion0 random # initial orientation
Each run will begin with a new, random initial orientation.
Initial quaternion, (x,y,z,w) = ( -0.425, -0.387, -0.614, 0.541 ),
DPF> dihe0 random # initial dihedrals (relative) or
random
DPF> torsdof 11 # torsional degrees of freedom
Number of torsional degrees of freedom = 11
Free energy coefficient for torsional degrees of freedom = 0.2983, the factory
default value.
Estimated loss of torsional free energy upon binding = +3.2813 kcal/mol
DPF> rmstol 2.0 # cluster_tolerance/A
Maximum RMS tolerance for conformational cluster analysis = 2.00 Angstroms
DPF> extnrg 1000.0 # external grid energy
External grid energy (beyond grid map walls) = 1000.00
DPF> e0max 0.0 10000 # max initial energy; max number of
retries
Using user-specified maximum number of retries for simanneal initialization,
10000 retries.
If the simanneal initial energy is greater than e0max, 0.000,
then a new, random initial state will be created.
DPF> ga_pop_size 150 # number of individuals in population
A population of 150 individuals will be used
DPF> ga_num_evals 2500000 # maximum number of energy evaluations
There will be at most 2500000 function evaluations used.
DPF> ga_num_generations 27000 # maximum number of generations
The GA will run for at most 27000 generations.
DPF> ga_elitism 1 # number of top individuals to
survive to next generation
The 1 best will be preserved each GA 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> sw_max_its 300 # iterations of Solis & Wets local
search
Solis & Wets algorithms will perform at most 300 iterations.
DPF> sw_max_succ 4 # consecutive successes before
changing rho
Solis & Wets algorithms expand rho every 4 in a row successes.
DPF> sw_max_fail 4 # consecutive failures before
changing rho
Solis & Wets algorithms contract rho every 4 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> unbound_model extended # state of unbound ligand
/home/comp/Apps/Autodock/autodock4: WARNING: Using autodock4.0 unbound extended
model in autodock4.2!
Computing the energy of the unbound state of the ligand,
given the torsion tree defined in the ligand file.
BEGINNING COMPUTATION OF UNBOUND EXTENDED STATE USING LGA
_________________________________________________________
Date: Tue Jun 5 09:17:05 2018
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 1000000 energy
evaluations.
Final-Value: -724.654
Finished Lamarckian Genetic Algorithm (LGA)
9:17 11" a.m., 06/05/2018
Total number of Energy Evaluations: 1000115
Total number of Generations: 625
Ligand Intramolecular Energy Analysis
=====================================
Non-bond Atom1-Atom2 Distance Total Elec vdW Hb
Desolv Sol_fn Type Dielectric
________ ___________ ________ ______ _________ ________ ________
________ ________ ____ __________
1 1-5 5.1670 -0.0128 +0.0000 -0.0124 +0.0000
-0.0004 +0.0472 1 25.867
2 1-6 6.3176 -0.0044 -0.0000 -0.0028 +0.0000
-0.0016 +0.0284 1 33.625
3 1-7 6.5207 -0.0032 +0.0000 -0.0033 +0.0000
+0.0001 +0.0257 1 35.010
4 1-8 7.5699 -0.0013 +0.0000 -0.0013 +0.0000
+0.0001 +0.0145 1 42.136
5 1-9 6.6080 -0.0029 +0.0000 -0.0030 +0.0000
+0.0001 +0.0245 1 35.613
6 1-13 5.2306 -0.0156 +0.0000 -0.0116 +0.0000
-0.0039 +0.0460 1 26.282
7 1-14 6.5884 -0.0033 +0.0000 -0.0031 +0.0000
-0.0002 +0.0248 1 35.484
8 1-15 7.7993 -0.0015 -0.0000 -0.0008 +0.0000
-0.0007 +0.0127 1 43.658
9 1-16 7.7919 -0.0011 +0.0000 -0.0011 +0.0000
+0.0000 +0.0127 1 43.605
10 1-17 8.9835 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0059 1 51.085
11 1-18 8.2707 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0095 1 46.703
12 2-6 4.8962 -0.0153 -0.0000 -0.0123 +0.0000
-0.0030 +0.0524 1 24.111
13 2-7 5.0069 -0.0144 +0.0000 -0.0146 +0.0000
+0.0002 +0.0503 1 24.825
14 2-8 6.1951 -0.0043 +0.0000 -0.0044 +0.0000
+0.0001 +0.0301 1 32.787
15 2-9 5.2658 -0.0110 +0.0000 -0.0112 +0.0000
+0.0002 +0.0454 1 26.517
16 2-12 5.0849 -0.0181 +0.0000 -0.0135 +0.0000
-0.0046 +0.0488 1 25.329
17 2-13 6.5002 -0.0055 +0.0000 -0.0033 +0.0000
-0.0022 +0.0259 1 34.878
18 2-14 7.7369 -0.0013 +0.0000 -0.0011 +0.0000
-0.0001 +0.0131 1 43.247
19 2-15 9.0461 -0.0003 -0.0000 +0.0000 +0.0000
-0.0003 +0.0056 1 51.452
20 2-16 9.1378 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0053 1 51.984
21 2-17 10.1411 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0025 1 57.421
22 2-18 9.5483 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0039 1 54.308
23 3-7 4.3770 -0.0237 +0.0003 -0.0242 +0.0000
+0.0003 +0.0631 1 20.847
24 3-8 5.0507 -0.0135 +0.0002 -0.0139 +0.0000
+0.0002 +0.0494 1 25.108
25 3-9 4.1950 -0.0243 +0.0003 -0.0249 +0.0000
+0.0003 +0.0671 1 19.739
26 3-11 5.2080 -0.0163 +0.0000 -0.0119 +0.0000
-0.0044 +0.0465 1 26.124
27 3-12 6.4828 -0.0058 +0.0000 -0.0034 +0.0000
-0.0025 +0.0262 1 34.746
28 3-13 7.8162 -0.0021 +0.0000 -0.0011 +0.0000
-0.0011 +0.0125 1 43.763
29 3-14 9.1357 +0.0000 +0.0000 +0.0000 +0.0000
-0.0000 +0.0053 1 51.974
30 3-15 10.3831 -0.0001 -0.0000 +0.0000 +0.0000
-0.0001 +0.0021 1 58.613
31 3-16 10.3686 +0.0001 +0.0000 +0.0000 +0.0000
+0.0000 +0.0021 1 58.547
32 3-17 11.5374 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0008 1 63.627
33 3-18 10.8366 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0014 1 60.714
34 4-10 4.9882 -0.0191 +0.0000 -0.0148 +0.0000
-0.0043 +0.0506 1 24.703
35 4-11 6.4049 -0.0060 +0.0000 -0.0036 +0.0000
-0.0023 +0.0272 1 34.214
36 4-12 7.5178 -0.0026 +0.0000 -0.0014 +0.0000
-0.0013 +0.0149 1 41.790
37 4-13 8.9494 -0.0004 +0.0001 +0.0000 +0.0000
-0.0005 +0.0060 1 50.879
38 4-14 10.1613 +0.0005 +0.0005 +0.0000 +0.0000
+0.0000 +0.0025 1 57.529
39 4-15 11.4902 -0.0002 -0.0001 +0.0000 +0.0000
-0.0000 +0.0008 1 63.442
40 4-16 11.5725 +0.0005 +0.0005 +0.0000 +0.0000
+0.0000 +0.0008 1 63.762
41 4-17 12.5587 +0.0004 +0.0004 +0.0000 +0.0000
+0.0000 +0.0003 1 67.171
42 4-18 11.9824 +0.0005 +0.0005 +0.0000 +0.0000
+0.0000 +0.0005 1 65.269
43 5-10 6.3812 -0.0040 +0.0000 -0.0037 +0.0000
-0.0002 +0.0275 1 34.063
44 5-11 7.7509 -0.0013 +0.0000 -0.0011 +0.0000
-0.0001 +0.0130 1 43.340
45 5-12 8.9159 -0.0000 +0.0000 +0.0000 +0.0000
-0.0001 +0.0062 1 50.681
46 5-13 10.3201 +0.0005 +0.0005 +0.0000 +0.0000
+0.0000 +0.0022 1 58.313
47 5-14 11.5626 +0.0036 +0.0035 +0.0000 +0.0000
+0.0001 +0.0008 1 63.726
48 5-15 12.8713 -0.0010 -0.0010 +0.0000 +0.0000
+0.0000 +0.0002 1 68.099
49 5-16 12.9492 +0.0034 +0.0034 +0.0000 +0.0000
+0.0000 +0.0002 1 68.319
50 5-17 13.9796 +0.0030 +0.0030 +0.0000 +0.0000
+0.0000 +0.0001 1 70.874
51 5-18 13.2824 +0.0033 +0.0032 +0.0000 +0.0000
+0.0000 +0.0001 1 69.220
52 6-10 7.4194 -0.0020 -0.0000 -0.0010 +0.0000
-0.0009 +0.0158 1 41.131
53 6-11 8.8564 -0.0004 -0.0000 +0.0000 +0.0000
-0.0004 +0.0064 1 50.324
54 6-12 9.9272 -0.0002 -0.0000 +0.0000 +0.0000
-0.0002 +0.0030 1 56.332
55 6-13 11.3831 -0.0002 -0.0001 +0.0000 +0.0000
-0.0000 +0.0009 1 63.021
56 6-14 12.5543 -0.0010 -0.0010 +0.0000 +0.0000
+0.0000 +0.0003 1 67.156
57 6-15 13.9103 +0.0003 +0.0003 +0.0000 +0.0000
-0.0000 +0.0001 1 70.722
58 6-16 14.0139 -0.0010 -0.0010 +0.0000 +0.0000
+0.0000 +0.0001 1 70.949
59 6-17 14.9415 -0.0009 -0.0009 +0.0000 +0.0000
+0.0000 +0.0000 1 72.715
60 6-18 14.4016 -0.0010 -0.0010 +0.0000 +0.0000
+0.0000 +0.0000 1 71.742
61 7-10 7.3776 -0.0015 +0.0000 -0.0015 +0.0000
+0.0001 +0.0162 1 40.847
62 7-11 8.8896 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0063 1 50.524
63 7-12 9.7685 +0.0001 +0.0000 +0.0000 +0.0000
+0.0000 +0.0033 1 55.498
64 7-13 11.2852 +0.0005 +0.0005 +0.0000 +0.0000
+0.0000 +0.0010 1 62.626
65 7-14 12.3214 +0.0037 +0.0036 +0.0000 +0.0000
+0.0000 +0.0004 1 66.419
66 7-15 13.7411 -0.0010 -0.0010 +0.0000 +0.0000
+0.0000 +0.0001 1 70.342
67 7-16 13.9791 +0.0035 +0.0035 +0.0000 +0.0000
+0.0000 +0.0001 1 70.874
68 7-17 14.6739 +0.0032 +0.0032 +0.0000 +0.0000
+0.0000 +0.0000 1 72.250
69 7-18 14.2560 +0.0034 +0.0034 +0.0000 +0.0000
+0.0000 +0.0001 1 71.453
70 8-10 8.7209 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0070 1 49.508
71 8-11 10.1344 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0025 1 57.390
72 8-12 11.2349 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0010 1 62.422
73 8-13 12.6764 +0.0004 +0.0004 +0.0000 +0.0000
+0.0000 +0.0003 1 67.529
74 8-14 13.8654 +0.0031 +0.0030 +0.0000 +0.0000
+0.0000 +0.0001 1 70.622
75 8-15 15.2111 -0.0009 -0.0009 +0.0000 +0.0000
+0.0000 +0.0000 1 73.151
76 8-16 15.3283 +0.0031 +0.0031 +0.0000 +0.0000
+0.0000 +0.0000 1 73.330
77 8-17 16.2729 +0.0028 +0.0028 +0.0000 +0.0000
+0.0000 +0.0000 1 74.579
78 8-18 15.6307 +0.0030 +0.0030 +0.0000 +0.0000
+0.0000 +0.0000 1 73.767
79 9-10 7.7350 -0.0011 +0.0000 -0.0011 +0.0000
+0.0000 +0.0132 1 43.233
80 9-11 9.1207 +0.0000 +0.0000 +0.0000 +0.0000
+0.0000 +0.0053 1 51.884
81 9-12 10.2264 +0.0001 +0.0000 +0.0000 +0.0000
+0.0000 +0.0023 1 57.850
82 9-13 11.6487 +0.0005 +0.0005 +0.0000 +0.0000
+0.0000 +0.0007 1 64.054
83 9-14 12.8416 +0.0034 +0.0034 +0.0000 +0.0000
+0.0000 +0.0002 1 68.012
84 9-15 14.1686 -0.0010 -0.0010 +0.0000 +0.0000
+0.0000 +0.0001 1 71.274
85 9-16 14.1495 +0.0034 +0.0034 +0.0000 +0.0000
+0.0000 +0.0001 1 71.235
86 9-17 15.1761 +0.0031 +0.0031 +0.0000 +0.0000
+0.0000 +0.0000 1 73.097
87 9-18 14.7779 +0.0032 +0.0032 +0.0000 +0.0000
+0.0000 +0.0000 1 72.435
88 10-14 5.2047 -0.0124 +0.0000 -0.0120 +0.0000
-0.0004 +0.0465 1 26.104
89 10-15 6.5033 -0.0038 -0.0000 -0.0023 +0.0000
-0.0015 +0.0259 1 34.894
90 10-16 6.6482 -0.0028 +0.0000 -0.0029 +0.0000
+0.0001 +0.0240 1 35.888
91 10-17 7.6128 -0.0012 +0.0000 -0.0013 +0.0000
+0.0001 +0.0141 1 42.423
92 10-18 7.0439 -0.0020 +0.0000 -0.0020 +0.0000
+0.0001 +0.0195 1 38.587
93 11-15 5.1898 -0.0116 -0.0000 -0.0089 +0.0000
-0.0027 +0.0468 1 26.006
94 11-16 5.2158 -0.0116 +0.0000 -0.0118 +0.0000
+0.0002 +0.0463 1 26.183
95 11-17 6.4108 -0.0035 +0.0000 -0.0036 +0.0000
+0.0001 +0.0271 1 34.264
96 11-18 5.7128 -0.0070 +0.0000 -0.0071 +0.0000
+0.0001 +0.0375 1 29.503
97 12-16 4.3247 -0.0241 +0.0003 -0.0247 +0.0000
+0.0003 +0.0643 1 20.517
98 12-17 5.0718 -0.0132 +0.0002 -0.0136 +0.0000
+0.0002 +0.0490 1 25.248
99 12-18 4.6273 -0.0201 +0.0002 -0.0206 +0.0000
+0.0003 +0.0579 1 22.400
________ ________ ________ ________
________
Total -0.3054 +0.0498 -0.3185 +0.0000
-0.0367
________ ________ ________ ________ ________
Total Elec vdW Hb
Desolv
Per-atom Intramolecular Energy Analysis
=======================================
Atom Type Total Elec vdW Hb Desolv
____ ___ ________ ________ ________ ________ ________
1 C -0.0229 +0.0000 -0.0196 +0.0000 -0.0033
2 C -0.0351 +0.0000 -0.0302 +0.0000 -0.0049
3 C -0.0429 +0.0005 -0.0397 +0.0000 -0.0036
4 C -0.0132 +0.0009 -0.0099 +0.0000 -0.0042
5 C -0.0026 +0.0064 -0.0086 +0.0000 -0.0004
6 N -0.0130 -0.0019 -0.0081 +0.0000 -0.0031
7 C -0.0147 +0.0068 -0.0218 +0.0000 +0.0004
8 C -0.0038 +0.0058 -0.0098 +0.0000 +0.0002
9 C -0.0133 +0.0065 -0.0201 +0.0000 +0.0003
10 C -0.0249 +0.0000 -0.0214 +0.0000 -0.0035
11 C -0.0288 +0.0000 -0.0241 +0.0000 -0.0047
12 C -0.0420 +0.0004 -0.0386 +0.0000 -0.0039
13 C -0.0109 +0.0009 -0.0080 +0.0000 -0.0038
14 C -0.0018 +0.0066 -0.0081 +0.0000 -0.0003
15 N -0.0106 -0.0019 -0.0060 +0.0000 -0.0027
16 C -0.0134 +0.0065 -0.0202 +0.0000 +0.0003
17 C -0.0031 +0.0059 -0.0093 +0.0000 +0.0002
18 C -0.0083 +0.0063 -0.0149 +0.0000 +0.0003
Total Intramolecular Interaction Energy = -0.305 kcal/mol
The internal energy of the unbound extended state was computed to be -0.305
kcal/mol
NOTE: The AutoDock internal energy of the "extended" state was negative.
NOTE: The unbound state was set to the "extended" state.
The internal energy of the unbound state was set to -0.305 kcal/mol
FINAL UNBOUND STATE
___________________
Detailed state: trans 4.144 71.448 72.730 quatxyzw 0.024719 0.047661 0.234268
0.970688 center 3.138 65.847 67.782 ntor 11 9.1080 37.5232 1.6422 20.1922
-29.2495 -6.5165 -4.6679 -146.7346 72.5714 -19.0086 111.0865
State: 4.144 71.448 72.730 0.103 0.198 0.975 27.813 9.11 37.52
1.64 20.19 -29.25 -6.52 -4.67 -146.73 72.57 -19.01 111.09
UNBOUND: MODEL 0
UNBOUND: USER Run = 0
UNBOUND: USER DPF = DME.dpf
UNBOUND: USER
UNBOUND: USER (1) Final Intermolecular Energy = +0.00 kcal/mol
UNBOUND: USER vdW + Hbond + desolv Energy = +0.00 kcal/mol
UNBOUND: USER Electrostatic Energy = +0.00 kcal/mol
UNBOUND: USER (2) Final Total Internal Energy = -0.31 kcal/mol
UNBOUND: USER (3) Torsional Free Energy = +3.28 kcal/mol
UNBOUND: USER (4) Unbound System's Energy = -0.31 kcal/mol
UNBOUND: USER
UNBOUND: USER
UNBOUND: USER NEWDPF move DME.pdbqt
UNBOUND: USER NEWDPF about 3.138400 65.846900 67.782300
UNBOUND: USER NEWDPF tran0 4.143889 71.447806 72.730398
UNBOUND: USER NEWDPF quaternion0 0.024719 0.047661 0.234268 0.970688
UNBOUND: USER NEWDPF axisangle0 0.102849 0.198306 0.974729 27.813440
UNBOUND: USER NEWDPF quat0 0.102849 0.198306 0.974729 27.813440
UNBOUND: USER NEWDPF dihe0 9.11 37.52 1.64 20.19 -29.25 -6.52 -4.67 -146.73
72.57 -19.01 111.09
UNBOUND: USER keepresnum = 1
UNBOUND: USER
UNBOUND: REMARK 11 active torsions:
UNBOUND: REMARK status: ('A' for Active; 'I' for Inactive)
UNBOUND: REMARK 1 A between atoms: N1_1 and C2_2
UNBOUND: REMARK 2 A between atoms: C2_2 and C3_3
UNBOUND: REMARK 3 A between atoms: C3_3 and C4_4
UNBOUND: REMARK 4 A between atoms: C4_4 and C5_5
UNBOUND: REMARK 5 A between atoms: C5_5 and C6_6
UNBOUND: REMARK 6 A between atoms: C6_6 and C7_7
UNBOUND: REMARK 7 A between atoms: C7_7 and C8_8
UNBOUND: REMARK 8 A between atoms: C8_8 and C9_9
UNBOUND: REMARK 9 A between atoms: C9_9 and C10_10
UNBOUND: REMARK 10 A between atoms: C10_10 and C11_11
UNBOUND: REMARK 11 A between atoms: C11_11 and N12_12
UNBOUND: USER x y z vdW Elec
q Type
UNBOUND: USER _______ _______ _______ _____ _____
______ ____
UNBOUND: ROOT
UNBOUND: ATOM 1 C6 DME A 999 5.555 70.377 74.037 +0.00 +0.00
+0.000 C
UNBOUND: ENDROOT
UNBOUND: BRANCH 1 2
UNBOUND: ATOM 2 C5 DME A 999 4.224 70.672 74.716 +0.00 +0.00
+0.000 C
UNBOUND: BRANCH 2 3
UNBOUND: ATOM 3 C4 DME A 999 3.869 69.759 75.908 +0.00 +0.00
+0.002 C
UNBOUND: BRANCH 3 4
UNBOUND: ATOM 4 C3 DME A 999 2.528 70.266 76.437 +0.00 +0.00
+0.028 C
UNBOUND: BRANCH 4 5
UNBOUND: ATOM 5 C2 DME A 999 1.603 69.296 77.185 +0.00 +0.00
+0.236 C
UNBOUND: BRANCH 5 6
UNBOUND: ATOM 6 N1 DME A 999 0.656 70.068 78.014 +0.00 +0.00
-0.079 N
UNBOUND: ATOM 7 C13 DME A 999 -0.097 71.072 77.214 +0.00 +0.00
+0.271 C
UNBOUND: ATOM 8 C14 DME A 999 -0.365 69.174 78.598 +0.00 +0.00
+0.271 C
UNBOUND: ATOM 9 C15 DME A 999 1.375 70.709 79.144 +0.00 +0.00
+0.271 C
UNBOUND: ENDBRANCH 5 6
UNBOUND: ENDBRANCH 4 5
UNBOUND: ENDBRANCH 3 4
UNBOUND: ENDBRANCH 2 3
UNBOUND: ENDBRANCH 1 2
UNBOUND: BRANCH 1 10
UNBOUND: ATOM 10 C7 DME A 999 5.863 71.286 72.870 +0.00 +0.00
+0.000 C
UNBOUND: BRANCH 10 11
UNBOUND: ATOM 11 C8 DME A 999 7.201 71.103 72.138 +0.00 +0.00
+0.000 C
UNBOUND: BRANCH 11 12
UNBOUND: ATOM 12 C9 DME A 999 7.320 72.086 70.938 +0.00 +0.00
+0.002 C
UNBOUND: BRANCH 12 13
UNBOUND: ATOM 13 C10 DME A 999 8.637 71.975 70.125 +0.00 +0.00
+0.028 C
UNBOUND: BRANCH 13 14
UNBOUND: ATOM 14 C11 DME A 999 8.829 72.946 68.929 +0.00 +0.00
+0.236 C
UNBOUND: BRANCH 14 15
UNBOUND: ATOM 15 N12 DME A 999 10.135 72.794 68.205 +0.00 +0.00
-0.079 N
UNBOUND: ATOM 16 C16 DME A 999 11.238 72.543 69.166 +0.00 +0.00
+0.271 C
UNBOUND: ATOM 17 C17 DME A 999 10.427 74.002 67.416 +0.00 +0.00
+0.271 C
UNBOUND: ATOM 18 C18 DME A 999 10.056 71.703 67.226 +0.00 +0.00
+0.271 C
UNBOUND: ENDBRANCH 14 15
UNBOUND: ENDBRANCH 13 14
UNBOUND: ENDBRANCH 12 13
UNBOUND: ENDBRANCH 11 12
UNBOUND: ENDBRANCH 10 11
UNBOUND: ENDBRANCH 1 10
UNBOUND: TORSDOF 11
UNBOUND: TER
UNBOUND: ENDMDL
________________________________________________________________________________
DPF> ga_run 10 # do this many hybrid GA-LS runs
centering ligand on specified point: 3.138 65.847 67.782
Furthest true ligand atom from "about" center is 7.048 Angstroms (maxrad).
Number of requested GA dockings = 10 runs
Unbound model to be used is 'extended' [AutoDock 4.0 default].
BEGINNING GENETIC ALGORITHM DOCKING 1 of 10
Run: 1 Seed: 1045835345 1754717119 [ Run 1 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.957
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 1.009 68.670 66.161 quatxyzw 0.359574 0.032328 -0.931956
0.033446 center 3.138 65.847 67.782 ntor 11 73.8796 100.9255 -49.6973 -12.8726
-179.7884 -180.0000 37.1533 -140.6113 -1.1413 74.3483 -154.1878
State: 1.009 68.670 66.161 0.360 0.032 -0.932 176.167 73.88 100.93
-49.70 -12.87 -179.79 -180.00 37.15 -140.61 -1.14 74.35 -154.19
DOCKED: MODEL 1
DOCKED: USER Run = 1
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -6.37 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 21.39 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -9.19 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.61 kcal/mol
DOCKED: USER Electrostatic Energy = -1.58 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.77 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 1.008903 68.669767 66.160815
DOCKED: USER NEWDPF quaternion0 0.359574 0.032328 -0.931956 0.033446
DOCKED: USER NEWDPF axisangle0 0.359775 0.032346 -0.932478 176.166664
DOCKED: USER NEWDPF quat0 0.359775 0.032346 -0.932478 176.166664
DOCKED: USER NEWDPF dihe0 73.88 100.93 -49.70 -12.87 -179.79 -180.00 37.15
-140.61 -1.14 74.35 -154.19
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 -1.107 69.128 65.760 -0.56 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 -0.714 69.355 67.214 -0.58 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 -0.059 70.719 67.521 -0.64 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 1.069 70.426 68.509 -0.60 -0.03
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 1.365 68.971 68.897 -0.32 -0.21
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 2.631 68.547 68.267 -0.35 +0.05
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 3.654 68.156 69.275 -0.29 -0.17
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 2.415 67.348 67.431 -0.17 -0.12
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 3.139 69.619 67.373 -0.31 -0.16
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 -0.199 68.173 65.023 -0.45 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 1.063 68.737 64.352 -0.43 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 0.763 69.201 62.897 -0.57 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 2.005 69.642 62.078 -0.54 -0.01
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 3.403 69.410 62.711 -0.30 -0.14
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 4.487 69.079 61.726 -0.43 +0.08
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 4.141 69.597 60.377 -0.37 -0.31
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 4.693 67.623 61.661 -0.30 -0.22
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 5.772 69.633 62.169 -0.42 -0.33
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 2 of 10
Run: 2 Seed: 1744285745 765030678 [ Run 2 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.726
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 2.988 66.454 67.813 quatxyzw -0.459043 0.278020
-0.248094 -0.806494 center 3.138 65.847 67.782 ntor 11 -8.0941 -107.1254
-51.2717 -24.2542 78.3610 32.9397 87.3280 -73.5427 -22.6891 97.5951 49.5267
State: 2.988 66.454 67.813 -0.776 0.470 -0.420 -72.490 -8.09 -107.13
-51.27 -24.25 78.36 32.94 87.33 -73.54 -22.69 97.60 49.53
DOCKED: MODEL 2
DOCKED: USER Run = 2
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -6.14 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 31.61 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -9.00 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.16 kcal/mol
DOCKED: USER Electrostatic Energy = -1.83 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.73 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 2.988178 66.453851 67.812689
DOCKED: USER NEWDPF quaternion0 -0.459043 0.278020 -0.248094 -0.806494
DOCKED: USER NEWDPF axisangle0 -0.776405 0.470231 -0.419616 -72.490362
DOCKED: USER NEWDPF quat0 -0.776405 0.470231 -0.419616 -72.490362
DOCKED: USER NEWDPF dihe0 -8.09 -107.13 -51.27 -24.25 78.36 32.94 87.33
-73.54 -22.69 97.60 49.53
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 5.040 65.742 68.169 -0.60 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 4.634 66.874 69.103 -0.64 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 3.444 66.569 70.038 -0.45 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 2.191 66.981 69.265 -0.45 -0.02
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 1.556 68.351 69.545 -0.27 -0.23
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 1.847 69.260 68.419 -0.39 +0.06
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 1.810 68.557 67.108 -0.19 -0.14
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 0.821 70.320 68.334 -0.37 -0.24
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 3.154 69.932 68.631 -0.37 -0.20
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 4.236 65.682 66.892 -0.45 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 4.968 65.900 65.559 -0.47 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 5.523 67.350 65.456 -0.46 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 4.751 68.282 64.483 -0.42 -0.02
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 5.584 69.243 63.595 -0.42 -0.19
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 5.160 69.288 62.155 -0.46 +0.08
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 5.949 70.302 61.411 -0.29 -0.40
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 3.726 69.602 62.054 -0.31 -0.19
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 5.312 67.968 61.533 -0.15 -0.34
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 3 of 10
Run: 3 Seed: 1834228679 1358019848 [ Run 3 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.639
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 4.192 64.426 68.498 quatxyzw -0.783677 -0.319243
-0.518961 -0.120888 center 3.138 65.847 67.782 ntor 11 -13.3320 177.3088
-51.9136 116.9916 -20.7536 143.9502 168.5134 -125.0604 29.9569 -171.3259
-171.8143
State: 4.192 64.426 68.498 -0.789 -0.322 -0.523 -166.113 -13.33
177.31 -51.91 116.99 -20.75 143.95 168.51 -125.06 29.96 -171.33 -171.81
DOCKED: MODEL 3
DOCKED: USER Run = 3
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -6.05 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 36.59 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -8.88 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.51 kcal/mol
DOCKED: USER Electrostatic Energy = -1.37 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.76 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 4.192084 64.426239 68.498016
DOCKED: USER NEWDPF quaternion0 -0.783677 -0.319243 -0.518961 -0.120888
DOCKED: USER NEWDPF axisangle0 -0.789467 -0.321601 -0.522795 -166.113304
DOCKED: USER NEWDPF quat0 -0.789467 -0.321601 -0.522795 -166.113304
DOCKED: USER NEWDPF dihe0 -13.33 177.31 -51.91 116.99 -20.75 143.95 168.51
-125.06 29.96 -171.33 -171.81
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 5.278 65.966 69.636 -0.71 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 5.322 66.198 68.131 -0.63 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 4.602 67.470 67.634 -0.47 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 3.859 68.029 68.847 -0.54 -0.02
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 3.372 69.485 68.819 -0.34 -0.17
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 1.909 69.504 68.623 -0.43 +0.06
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 1.246 68.325 69.244 -0.26 -0.25
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 1.316 70.688 69.280 -0.33 -0.31
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 1.590 69.600 67.176 -0.25 -0.16
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 4.998 64.535 70.028 -0.68 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 3.596 64.183 70.549 -0.47 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 2.531 65.179 70.006 -0.44 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 1.228 65.269 70.843 -0.44 -0.02
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 0.797 64.009 71.641 -0.25 -0.15
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 0.020 63.001 70.845 -0.37 +0.04
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 0.900 61.882 70.421 -0.25 -0.11
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 -0.581 63.637 69.662 -0.32 -0.14
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 -1.112 62.489 71.627 -0.31 -0.15
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 4 of 10
Run: 4 Seed: 1437051228 1857411358 [ Run 4 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.581
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 3.728 65.538 66.224 quatxyzw 0.680363 0.145494 -0.003296
0.718280 center 3.138 65.847 67.782 ntor 11 177.0302 53.2933 109.7504 77.8141
-52.3662 -69.0023 -58.6320 -73.4356 40.0862 -68.6369 -56.6287
State: 3.728 65.538 66.224 0.978 0.209 -0.005 88.175 177.03 53.29
109.75 77.81 -52.37 -69.00 -58.63 -73.44 40.09 -68.64 -56.63
DOCKED: MODEL 4
DOCKED: USER Run = 4
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -5.99 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 40.39 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -8.89 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.17 kcal/mol
DOCKED: USER Electrostatic Energy = -1.73 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.69 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 3.727731 65.537635 66.224054
DOCKED: USER NEWDPF quaternion0 0.680363 0.145494 -0.003296 0.718280
DOCKED: USER NEWDPF axisangle0 0.977879 0.209116 -0.004738 88.174667
DOCKED: USER NEWDPF quat0 0.977879 0.209116 -0.004738 88.174667
DOCKED: USER NEWDPF dihe0 177.03 53.29 109.75 77.81 -52.37 -69.00 -58.63
-73.44 40.09 -68.64 -56.63
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 5.216 66.975 66.975 -0.46 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 3.785 67.480 67.102 -0.42 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 3.356 67.910 68.521 -0.51 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 2.860 69.350 68.389 -0.54 -0.02
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 1.509 69.735 69.007 -0.36 -0.23
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 0.450 69.591 67.988 -0.40 +0.06
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 -0.512 70.727 68.019 -0.38 -0.25
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 1.036 69.599 66.631 -0.22 -0.15
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 -0.246 68.291 68.158 -0.24 -0.17
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 5.396 65.900 65.929 -0.47 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 4.232 65.618 64.967 -0.45 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 4.709 65.652 63.486 -0.50 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 4.268 66.905 62.683 -0.45 -0.01
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 5.383 67.825 62.117 -0.32 -0.23
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 5.294 69.257 62.558 -0.47 +0.08
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 3.902 69.595 62.953 -0.27 -0.17
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 5.736 70.154 61.479 -0.32 -0.38
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 6.214 69.510 63.674 -0.41 -0.25
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 5 of 10
Run: 5 Seed: 529128612 218814117 [ Run 5 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.840
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 3.456 68.517 65.742 quatxyzw -0.558263 0.677051 0.046543
-0.477261 center 3.138 65.847 67.782 ntor 11 177.2855 77.8741 68.6930 89.1764
-64.8617 177.5792 176.1113 126.4841 127.9445 158.7118 147.7273
State: 3.456 68.517 65.742 -0.635 0.770 0.053 -122.987 177.29
77.87 68.69 89.18 -64.86 177.58 176.11 126.48 127.94 158.71 147.73
DOCKED: MODEL 5
DOCKED: USER Run = 5
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -6.25 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 26.09 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -8.77 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.34 kcal/mol
DOCKED: USER Electrostatic Energy = -1.44 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -1.07 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 3.455546 68.516506 65.741607
DOCKED: USER NEWDPF quaternion0 -0.558263 0.677051 0.046543 -0.477261
DOCKED: USER NEWDPF axisangle0 -0.635284 0.770460 0.052965 -122.986701
DOCKED: USER NEWDPF quat0 -0.635284 0.770460 0.052965 -122.986701
DOCKED: USER NEWDPF dihe0 177.29 77.87 68.69 89.18 -64.86 177.58 176.11
126.48 127.94 158.71 147.73
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 4.535 67.720 63.996 -0.40 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 5.205 68.947 64.600 -0.49 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 5.935 69.866 63.599 -0.70 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 5.762 69.211 62.229 -0.62 -0.03
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 5.019 69.974 61.123 -0.35 -0.31
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 4.050 69.068 60.474 -0.52 +0.09
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 4.052 69.218 58.993 -0.28 -0.31
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 4.409 67.658 60.733 -0.25 -0.26
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 2.693 69.286 61.035 -0.30 -0.17
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 3.065 67.601 64.323 -0.33 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 2.475 66.198 64.527 -0.43 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 3.537 65.098 64.241 -0.53 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 4.322 64.601 65.484 -0.45 -0.01
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 3.891 65.148 66.872 -0.26 -0.11
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 4.895 66.054 67.524 -0.41 +0.03
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 6.082 66.231 66.650 -0.26 -0.11
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 5.313 65.503 68.823 -0.46 -0.11
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 4.290 67.355 67.832 -0.29 -0.13
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 6 of 10
Run: 6 Seed: 1541331764 1908369762 [ Run 6 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.425
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 6.658 64.393 68.963 quatxyzw -0.223839 -0.629814
0.590340 -0.452471 center 3.138 65.847 67.782 ntor 11 -51.4037 173.3120
102.5136 51.1728 -48.0633 -44.5617 -24.1960 -145.7996 158.8216 27.7522 57.5332
State: 6.658 64.393 68.963 -0.251 -0.706 0.662 -126.195 -51.40
173.31 102.51 51.17 -48.06 -44.56 -24.20 -145.80 158.82 27.75 57.53
DOCKED: MODEL 6
DOCKED: USER Run = 6
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -5.84 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 52.57 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -8.97 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.91 kcal/mol
DOCKED: USER Electrostatic Energy = -1.07 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.45 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 6.657537 64.393433 68.962612
DOCKED: USER NEWDPF quaternion0 -0.223839 -0.629814 0.590340 -0.452471
DOCKED: USER NEWDPF axisangle0 -0.251003 -0.706244 0.661980 -126.195399
DOCKED: USER NEWDPF quat0 -0.251003 -0.706244 0.661980 -126.195399
DOCKED: USER NEWDPF dihe0 -51.40 173.31 102.51 51.17 -48.06 -44.56 -24.20
-145.80 158.82 27.75 57.53
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 4.900 65.251 69.974 -0.68 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 4.931 63.729 70.024 -0.60 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 3.774 63.016 69.294 -0.50 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 4.268 61.597 69.014 -0.52 -0.01
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 3.332 60.412 69.285 -0.40 -0.06
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 3.688 59.796 70.579 -0.39 +0.02
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 4.916 60.400 71.165 -0.37 -0.04
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 2.617 60.026 71.571 -0.17 -0.09
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 3.833 58.327 70.422 -0.43 -0.07
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 5.716 65.843 68.850 -0.69 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 5.019 66.797 67.868 -0.55 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 5.407 66.467 66.397 -0.51 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 4.776 67.397 65.326 -0.39 -0.01
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 5.645 67.770 64.096 -0.26 -0.15
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 5.346 69.118 63.506 -0.45 +0.06
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 6.290 70.137 64.031 -0.37 -0.23
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 3.963 69.515 63.814 -0.27 -0.16
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 5.417 69.065 62.041 -0.35 -0.32
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 7 of 10
Run: 7 Seed: 2060194629 1761548966 [ Run 7 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.424
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 4.564 69.075 65.919 quatxyzw -0.189420 0.944520
-0.132583 0.233291 center 3.138 65.847 67.782 ntor 11 -17.5640 141.3132 99.3965
66.2365 164.1168 -7.7917 64.5121 -83.7438 -44.2956 -150.1850 162.2920
State: 4.564 69.075 65.919 -0.195 0.971 -0.136 153.018 -17.56 141.31
99.40 66.24 164.12 -7.79 64.51 -83.74 -44.30 -150.19 162.29
DOCKED: MODEL 7
DOCKED: USER Run = 7
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -5.84 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 52.64 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -8.70 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.14 kcal/mol
DOCKED: USER Electrostatic Energy = -1.57 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.72 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 4.563839 69.074839 65.918829
DOCKED: USER NEWDPF quaternion0 -0.189420 0.944520 -0.132583 0.233291
DOCKED: USER NEWDPF axisangle0 -0.194795 0.971321 -0.136345 153.018247
DOCKED: USER NEWDPF quat0 -0.194795 0.971321 -0.136345 153.018247
DOCKED: USER NEWDPF dihe0 -17.56 141.31 99.40 66.24 164.12 -7.79 64.51
-83.74 -44.30 -150.19 162.29
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 2.740 67.842 65.942 -0.34 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 3.597 67.612 64.704 -0.33 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 5.120 67.569 64.949 -0.44 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 5.687 68.815 64.270 -0.52 -0.02
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 4.795 69.617 63.313 -0.38 -0.17
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 5.181 69.314 61.920 -0.47 +0.09
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 5.764 67.951 61.786 -0.17 -0.36
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 3.993 69.328 61.041 -0.37 -0.26
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 6.114 70.350 61.413 -0.29 -0.41
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 2.981 69.172 66.616 -0.45 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 3.223 69.188 68.133 -0.54 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 4.256 68.099 68.545 -0.54 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 3.704 66.991 69.481 -0.53 -0.02
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 4.682 65.871 69.925 -0.44 -0.11
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 4.120 64.482 69.842 -0.42 +0.03
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 3.826 64.122 68.432 -0.27 -0.12
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 2.893 64.377 70.648 -0.24 -0.13
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 5.053 63.513 70.431 -0.40 -0.09
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 8 of 10
Run: 8 Seed: 1669994647 585559122 [ Run 8 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.327
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 3.274 66.243 68.993 quatxyzw 0.263935 0.227920 0.001394
-0.937224 center 3.138 65.847 67.782 ntor 11 -153.5775 169.7898 64.3521 1.2992
-48.7083 23.5047 24.1147 -97.8374 101.0972 105.1119 -172.4787
State: 3.274 66.243 68.993 0.757 0.654 0.004 -40.819 -153.58 169.79
64.35 1.30 -48.71 23.50 24.11 -97.84 101.10 105.11 -172.48
DOCKED: MODEL 8
DOCKED: USER Run = 8
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -5.74 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 62.03 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -8.93 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.81 kcal/mol
DOCKED: USER Electrostatic Energy = -1.12 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.40 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 3.273732 66.243324 68.992534
DOCKED: USER NEWDPF quaternion0 0.263935 0.227920 0.001394 -0.937224
DOCKED: USER NEWDPF axisangle0 0.756851 0.653576 0.003997 -40.819049
DOCKED: USER NEWDPF quat0 0.756851 0.653576 0.003997 -40.819049
DOCKED: USER NEWDPF dihe0 -153.58 169.79 64.35 1.30 -48.71 23.50 24.11
-97.84 101.10 105.11 -172.48
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 5.385 65.632 68.866 -0.71 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 4.573 64.770 69.823 -0.62 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 5.381 63.732 70.631 -0.62 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 4.406 62.596 70.942 -0.53 -0.01
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 4.862 61.144 70.744 -0.41 -0.04
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 3.767 60.372 70.122 -0.41 +0.02
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 3.140 59.422 71.081 -0.27 -0.08
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 2.682 61.275 69.686 -0.28 -0.09
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 4.264 59.667 68.913 -0.37 -0.02
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 4.787 66.996 68.613 -0.60 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 4.095 67.250 67.265 -0.44 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 5.072 67.001 66.080 -0.46 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 5.123 68.135 65.021 -0.42 -0.02
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 5.424 67.734 63.552 -0.27 -0.16
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 5.010 68.753 62.530 -0.40 +0.07
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 6.140 69.664 62.216 -0.43 -0.35
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 3.864 69.534 63.021 -0.27 -0.17
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 4.534 68.093 61.308 -0.32 -0.27
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 9 of 10
Run: 9 Seed: 679106909 254368675 [ Run 9 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.871
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 0.942 69.542 65.583 quatxyzw 0.371640 -0.288731
-0.755676 -0.455491 center 3.138 65.847 67.782 ntor 11 113.9883 -5.4308 83.7311
-45.8519 140.3853 173.9741 -74.0498 -180.0000 178.4445 176.4039 -170.5369
State: 0.942 69.542 65.583 0.417 -0.324 -0.849 -125.807 113.99
-5.43 83.73 -45.85 140.39 173.97 -74.05 -180.00 178.44 176.40 -170.54
DOCKED: MODEL 9
DOCKED: USER Run = 9
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -6.28 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 24.75 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -9.14 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.46 kcal/mol
DOCKED: USER Electrostatic Energy = -1.68 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.73 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 0.942075 69.542238 65.582726
DOCKED: USER NEWDPF quaternion0 0.371640 -0.288731 -0.755676 -0.455491
DOCKED: USER NEWDPF axisangle0 0.417460 -0.324329 -0.848845 -125.806967
DOCKED: USER NEWDPF quat0 0.417460 -0.324329 -0.848845 -125.806967
DOCKED: USER NEWDPF dihe0 113.99 -5.43 83.73 -45.85 140.39 173.97 -74.05
-180.00 178.44 176.40 -170.54
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 -0.712 68.104 65.379 -0.45 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 -1.163 69.456 65.915 -0.53 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 -1.292 69.553 67.450 -0.56 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 -0.141 70.447 67.910 -0.62 -0.02
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 1.211 70.357 67.188 -0.24 -0.15
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 2.248 69.935 68.150 -0.46 +0.06
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 3.440 69.360 67.469 -0.28 -0.15
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 2.746 71.098 68.914 -0.45 -0.23
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 1.675 68.978 69.130 -0.29 -0.25
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 0.756 67.820 65.590 -0.41 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 1.705 67.957 64.390 -0.39 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 1.012 68.699 63.211 -0.51 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 1.952 69.578 62.343 -0.53 -0.01
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 3.460 69.597 62.709 -0.29 -0.14
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 4.359 68.970 61.683 -0.42 +0.07
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 4.387 67.494 61.846 -0.29 -0.17
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 5.724 69.509 61.801 -0.35 -0.38
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 3.919 69.324 60.328 -0.38 -0.29
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
BEGINNING GENETIC ALGORITHM DOCKING 10 of 10
Run: 10 Seed: 1602514 1948296098 [ Run 10 of 10 GA/GALS ]
Beginning LAMARCKIAN GENETIC ALGORITHM (LGA), with a maximum of 2500000 energy
evaluations.
Final-Value: -9.644
FINAL GENETIC ALGORITHM DOCKED STATE
_______________________________________________
Detailed state: trans 5.619 67.926 65.960 quatxyzw -0.118073 0.261817 0.816004
0.501645 center 3.138 65.847 67.782 ntor 11 -175.0259 -164.0552 -51.8844
102.2864 177.4368 -179.7364 39.3395 180.0000 149.7208 114.9978 -153.8497
State: 5.619 67.926 65.960 -0.136 0.303 0.943 119.782 -175.03 -164.06
-51.88 102.29 177.44 -179.74 39.34 180.00 149.72 115.00 -153.85
DOCKED: MODEL 10
DOCKED: USER Run = 10
DOCKED: USER DPF = DME.dpf
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -6.06 kcal/mol
[=(1)+(2)+(3)-(4)]
DOCKED: USER Estimated Inhibition Constant, Ki = 36.32 uM (micromolar)
[Temperature = 298.15 K]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -8.88 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -7.23 kcal/mol
DOCKED: USER Electrostatic Energy = -1.65 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = -0.76 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +3.28 kcal/mol
DOCKED: USER (4) Unbound System's Energy = -0.31 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: USER NEWDPF move DME.pdbqt
DOCKED: USER NEWDPF about 3.138400 65.846900 67.782300
DOCKED: USER NEWDPF tran0 5.618897 67.926168 65.959955
DOCKED: USER NEWDPF quaternion0 -0.118073 0.261817 0.816004 0.501645
DOCKED: USER NEWDPF axisangle0 -0.136489 0.302653 0.943277 119.782164
DOCKED: USER NEWDPF quat0 -0.136489 0.302653 0.943277 119.782164
DOCKED: USER NEWDPF dihe0 -175.03 -164.06 -51.88 102.29 177.44 -179.74 39.34
180.00 149.72 115.00 -153.85
DOCKED: USER keepresnum = 1
DOCKED: USER
DOCKED: REMARK 11 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: N1_1 and C2_2
DOCKED: REMARK 2 A between atoms: C2_2 and C3_3
DOCKED: REMARK 3 A between atoms: C3_3 and C4_4
DOCKED: REMARK 4 A between atoms: C4_4 and C5_5
DOCKED: REMARK 5 A between atoms: C5_5 and C6_6
DOCKED: REMARK 6 A between atoms: C6_6 and C7_7
DOCKED: REMARK 7 A between atoms: C7_7 and C8_8
DOCKED: REMARK 8 A between atoms: C8_8 and C9_9
DOCKED: REMARK 9 A between atoms: C9_9 and C10_10
DOCKED: REMARK 10 A between atoms: C10_10 and C11_11
DOCKED: REMARK 11 A between atoms: C11_11 and N12_12
DOCKED: USER x y z vdW Elec
q Type
DOCKED: USER _______ _______ _______ _____ _____
______ ____
DOCKED: ROOT
DOCKED: ATOM 1 C6 DME A 999 3.979 66.744 66.832 -0.41 -0.00
+0.000 C
DOCKED: ENDROOT
DOCKED: BRANCH 1 2
DOCKED: ATOM 2 C5 DME A 999 3.920 68.216 67.217 -0.44 -0.00
+0.000 C
DOCKED: BRANCH 2 3
DOCKED: ATOM 3 C4 DME A 999 3.866 68.505 68.732 -0.54 -0.00
+0.002 C
DOCKED: BRANCH 3 4
DOCKED: ATOM 4 C3 DME A 999 2.830 69.615 68.908 -0.56 -0.02
+0.028 C
DOCKED: BRANCH 4 5
DOCKED: ATOM 5 C2 DME A 999 2.100 70.160 67.672 -0.34 -0.16
+0.236 C
DOCKED: BRANCH 5 6
DOCKED: ATOM 6 N1 DME A 999 0.716 69.645 67.659 -0.39 +0.05
-0.079 N
DOCKED: ATOM 7 C13 DME A 999 0.356 69.042 66.347 -0.24 -0.14
+0.271 C
DOCKED: ATOM 8 C14 DME A 999 0.559 68.563 68.654 -0.22 -0.21
+0.271 C
DOCKED: ATOM 9 C15 DME A 999 -0.232 70.725 68.032 -0.39 -0.25
+0.271 C
DOCKED: ENDBRANCH 5 6
DOCKED: ENDBRANCH 4 5
DOCKED: ENDBRANCH 3 4
DOCKED: ENDBRANCH 2 3
DOCKED: ENDBRANCH 1 2
DOCKED: BRANCH 1 10
DOCKED: ATOM 10 C7 DME A 999 5.352 66.275 66.411 -0.52 -0.00
+0.000 C
DOCKED: BRANCH 10 11
DOCKED: ATOM 11 C8 DME A 999 5.761 66.444 64.940 -0.51 -0.00
+0.000 C
DOCKED: BRANCH 11 12
DOCKED: ATOM 12 C9 DME A 999 4.645 65.929 63.987 -0.48 -0.00
+0.002 C
DOCKED: BRANCH 12 13
DOCKED: ATOM 13 C10 DME A 999 4.521 66.697 62.644 -0.45 -0.01
+0.028 C
DOCKED: BRANCH 13 14
DOCKED: ATOM 14 C11 DME A 999 5.613 67.749 62.313 -0.25 -0.23
+0.236 C
DOCKED: BRANCH 14 15
DOCKED: ATOM 15 N12 DME A 999 5.224 69.168 62.613 -0.45 +0.07
-0.079 N
DOCKED: ATOM 16 C16 DME A 999 6.142 69.757 63.621 -0.45 -0.24
+0.271 C
DOCKED: ATOM 17 C17 DME A 999 3.840 69.225 63.108 -0.27 -0.16
+0.271 C
DOCKED: ATOM 18 C18 DME A 999 5.231 69.973 61.386 -0.34 -0.35
+0.271 C
DOCKED: ENDBRANCH 14 15
DOCKED: ENDBRANCH 13 14
DOCKED: ENDBRANCH 12 13
DOCKED: ENDBRANCH 11 12
DOCKED: ENDBRANCH 10 11
DOCKED: ENDBRANCH 1 10
DOCKED: TORSDOF 11
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
DPF> analysis # perform a ranked cluster analysis
CLUSTER ANALYSIS OF CONFORMATIONS
_________________________________
Number of conformations = 10
RMSD cluster analysis will be performed using the ligand atoms only (18 / 18
total atoms).
Outputting structurally similar clusters, ranked in order of increasing energy.
________________________________________________________________________________
Number of distinct conformational clusters found = 4, out of 10 runs,
Using an rmsd-tolerance of 2.0 A
CLUSTERING HISTOGRAM
____________________
________________________________________________________________________________
| | | | |
Clus | Lowest | Run | Mean | Num | Histogram
-ter | Binding | | Binding | in |
Rank | Energy | | Energy | Clus| 5 10 15 20 25 30 35
_____|___________|_____|___________|_____|____:____|____:____|____:____|____:___
1 | -6.37 | 1 | -6.17 | 5 |#####
2 | -6.25 | 5 | -6.05 | 2 |##
3 | -6.05 | 3 | -6.05 | 1 |#
4 | -5.84 | 6 | -5.79 | 2 |##
_____|___________|_____|___________|_____|______________________________________
Number of multi-member conformational clusters found = 3, out of 10 runs.
RMSD TABLE
__________
_____________________________________________________________________
| | | | | |
Rank | Sub- | Run | Binding | Cluster | Reference | Grep
| Rank | | Energy | RMSD | RMSD | Pattern
_____|______|______|___________|_________|_________________|___________
1 1 1 -6.37 0.00 3.11 RANKING
1 2 9 -6.28 0.82 3.30 RANKING
1 3 2 -6.14 1.93 2.33 RANKING
1 4 10 -6.06 1.81 2.53 RANKING
1 5 4 -5.99 1.90 2.71 RANKING
2 1 5 -6.25 0.00 2.31 RANKING
2 2 7 -5.84 1.83 1.74 RANKING
3 1 3 -6.05 0.00 2.30 RANKING
4 1 6 -5.84 0.00 2.29 RANKING
4 2 8 -5.74 0.98 2.18 RANKING
_______________________________________________________________________
INFORMATION ENTROPY ANALYSIS FOR THIS CLUSTERING
________________________________________________
Information entropy for this clustering = 0.53 (rmstol = 2.00 Angstrom)
_______________________________________________________________________
STATISTICAL MECHANICAL ANALYSIS
_______________________________
Partition function, Q = 10.10 at Temperature, T = 298.15 K
Free energy, A ~ -1370.30 kcal/mol at Temperature, T = 298.15 K
Internal energy, U = -6.06 kcal/mol at Temperature, T = 298.15 K
Entropy, S = 4.58 kcal/mol/K at Temperature, T = 298.15 K
_______________________________________________________________________
LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER
___________________________________________________
Keeping original residue number (specified in the input PDBQ file) for
outputting.
MODEL 1
USER Run = 1
USER Cluster Rank = 1
USER Number of conformations in this cluster = 5
USER
USER RMSD from reference structure = 3.110 A
USER
USER Estimated Free Energy of Binding = -6.37 kcal/mol
[=(1)+(2)+(3)-(4)]
USER Estimated Inhibition Constant, Ki = 21.39 uM (micromolar)
[Temperature = 298.15 K]
USER
USER (1) Final Intermolecular Energy = -9.19 kcal/mol
USER vdW + Hbond + desolv Energy = -7.61 kcal/mol
USER Electrostatic Energy = -1.58 kcal/mol
USER (2) Final Total Internal Energy = -0.77 kcal/mol
USER (3) Torsional Free Energy = +3.28 kcal/mol
USER (4) Unbound System's Energy = -0.31 kcal/mol
USER
USER
USER
USER DPF = DME.dpf
USER NEWDPF move DME.pdbqt
USER NEWDPF about 3.138400 65.846900 67.782300
USER NEWDPF tran0 1.008903 68.669767 66.160815
USER NEWDPF axisangle0 0.359775 0.032346 -0.932478 176.166664
USER NEWDPF quaternion0 0.359574 0.032328 -0.931956 0.033446
USER NEWDPF dihe0 73.88 100.93 -49.70 -12.87 -179.79 -180.00 37.15
-140.61 -1.14 74.35 -154.19
USER
USER x y z vdW Elec q
RMS
ATOM 1 C6 DME A 999 -1.107 69.128 65.760 -0.56 -0.00 +0.000
3.110
ATOM 2 C5 DME A 999 -0.714 69.355 67.214 -0.58 -0.00 +0.000
3.110
ATOM 3 C4 DME A 999 -0.059 70.719 67.521 -0.64 -0.00 +0.002
3.110
ATOM 4 C3 DME A 999 1.069 70.426 68.509 -0.60 -0.03 +0.028
3.110
ATOM 5 C2 DME A 999 1.365 68.971 68.897 -0.32 -0.21 +0.236
3.110
ATOM 6 N1 DME A 999 2.631 68.547 68.267 -0.35 +0.05 -0.079
3.110
ATOM 7 C13 DME A 999 3.654 68.156 69.275 -0.29 -0.17 +0.271
3.110
ATOM 8 C14 DME A 999 2.415 67.348 67.431 -0.17 -0.12 +0.271
3.110
ATOM 9 C15 DME A 999 3.139 69.619 67.373 -0.31 -0.16 +0.271
3.110
ATOM 10 C7 DME A 999 -0.199 68.173 65.023 -0.45 -0.00 +0.000
3.110
ATOM 11 C8 DME A 999 1.063 68.737 64.352 -0.43 -0.00 +0.000
3.110
ATOM 12 C9 DME A 999 0.763 69.201 62.897 -0.57 -0.00 +0.002
3.110
ATOM 13 C10 DME A 999 2.005 69.642 62.078 -0.54 -0.01 +0.028
3.110
ATOM 14 C11 DME A 999 3.403 69.410 62.711 -0.30 -0.14 +0.236
3.110
ATOM 15 N12 DME A 999 4.487 69.079 61.726 -0.43 +0.08 -0.079
3.110
ATOM 16 C16 DME A 999 4.141 69.597 60.377 -0.37 -0.31 +0.271
3.110
ATOM 17 C17 DME A 999 4.693 67.623 61.661 -0.30 -0.22 +0.271
3.110
ATOM 18 C18 DME A 999 5.772 69.633 62.169 -0.42 -0.33 +0.271
3.110
TER
ENDMDL
MODEL 5
USER Run = 5
USER Cluster Rank = 2
USER Number of conformations in this cluster = 2
USER
USER RMSD from reference structure = 2.306 A
USER
USER Estimated Free Energy of Binding = -6.25 kcal/mol
[=(1)+(2)+(3)-(4)]
USER Estimated Inhibition Constant, Ki = 26.09 uM (micromolar)
[Temperature = 298.15 K]
USER
USER (1) Final Intermolecular Energy = -8.77 kcal/mol
USER vdW + Hbond + desolv Energy = -7.34 kcal/mol
USER Electrostatic Energy = -1.44 kcal/mol
USER (2) Final Total Internal Energy = -1.07 kcal/mol
USER (3) Torsional Free Energy = +3.28 kcal/mol
USER (4) Unbound System's Energy = -0.31 kcal/mol
USER
USER
USER
USER DPF = DME.dpf
USER NEWDPF move DME.pdbqt
USER NEWDPF about 3.138400 65.846900 67.782300
USER NEWDPF tran0 3.455546 68.516506 65.741607
USER NEWDPF axisangle0 -0.635284 0.770460 0.052965 -122.986701
USER NEWDPF quaternion0 -0.558263 0.677051 0.046543 -0.477261
USER NEWDPF dihe0 177.29 77.87 68.69 89.18 -64.86 177.58 176.11 126.48
127.94 158.71 147.73
USER
USER x y z vdW Elec q
RMS
ATOM 1 C6 DME A 999 4.535 67.720 63.996 -0.40 -0.00 +0.000
2.306
ATOM 2 C5 DME A 999 5.205 68.947 64.600 -0.49 -0.00 +0.000
2.306
ATOM 3 C4 DME A 999 5.935 69.866 63.599 -0.70 -0.00 +0.002
2.306
ATOM 4 C3 DME A 999 5.762 69.211 62.229 -0.62 -0.03 +0.028
2.306
ATOM 5 C2 DME A 999 5.019 69.974 61.123 -0.35 -0.31 +0.236
2.306
ATOM 6 N1 DME A 999 4.050 69.068 60.474 -0.52 +0.09 -0.079
2.306
ATOM 7 C13 DME A 999 4.052 69.218 58.993 -0.28 -0.31 +0.271
2.306
ATOM 8 C14 DME A 999 4.409 67.658 60.733 -0.25 -0.26 +0.271
2.306
ATOM 9 C15 DME A 999 2.693 69.286 61.035 -0.30 -0.17 +0.271
2.306
ATOM 10 C7 DME A 999 3.065 67.601 64.323 -0.33 -0.00 +0.000
2.306
ATOM 11 C8 DME A 999 2.475 66.198 64.527 -0.43 -0.00 +0.000
2.306
ATOM 12 C9 DME A 999 3.537 65.098 64.241 -0.53 -0.00 +0.002
2.306
ATOM 13 C10 DME A 999 4.322 64.601 65.484 -0.45 -0.01 +0.028
2.306
ATOM 14 C11 DME A 999 3.891 65.148 66.872 -0.26 -0.11 +0.236
2.306
ATOM 15 N12 DME A 999 4.895 66.054 67.524 -0.41 +0.03 -0.079
2.306
ATOM 16 C16 DME A 999 6.082 66.231 66.650 -0.26 -0.11 +0.271
2.306
ATOM 17 C17 DME A 999 5.313 65.503 68.823 -0.46 -0.11 +0.271
2.306
ATOM 18 C18 DME A 999 4.290 67.355 67.832 -0.29 -0.13 +0.271
2.306
TER
ENDMDL
MODEL 3
USER Run = 3
USER Cluster Rank = 3
USER Number of conformations in this cluster = 1
USER
USER RMSD from reference structure = 2.300 A
USER
USER Estimated Free Energy of Binding = -6.05 kcal/mol
[=(1)+(2)+(3)-(4)]
USER Estimated Inhibition Constant, Ki = 36.59 uM (micromolar)
[Temperature = 298.15 K]
USER
USER (1) Final Intermolecular Energy = -8.88 kcal/mol
USER vdW + Hbond + desolv Energy = -7.51 kcal/mol
USER Electrostatic Energy = -1.37 kcal/mol
USER (2) Final Total Internal Energy = -0.76 kcal/mol
USER (3) Torsional Free Energy = +3.28 kcal/mol
USER (4) Unbound System's Energy = -0.31 kcal/mol
USER
USER
USER
USER DPF = DME.dpf
USER NEWDPF move DME.pdbqt
USER NEWDPF about 3.138400 65.846900 67.782300
USER NEWDPF tran0 4.192084 64.426239 68.498016
USER NEWDPF axisangle0 -0.789467 -0.321601 -0.522795 -166.113304
USER NEWDPF quaternion0 -0.783677 -0.319243 -0.518961 -0.120888
USER NEWDPF dihe0 -13.33 177.31 -51.91 116.99 -20.75 143.95 168.51
-125.06 29.96 -171.33 -171.81
USER
USER x y z vdW Elec q
RMS
ATOM 1 C6 DME A 999 5.278 65.966 69.636 -0.71 -0.00 +0.000
2.300
ATOM 2 C5 DME A 999 5.322 66.198 68.131 -0.63 -0.00 +0.000
2.300
ATOM 3 C4 DME A 999 4.602 67.470 67.634 -0.47 -0.00 +0.002
2.300
ATOM 4 C3 DME A 999 3.859 68.029 68.847 -0.54 -0.02 +0.028
2.300
ATOM 5 C2 DME A 999 3.372 69.485 68.819 -0.34 -0.17 +0.236
2.300
ATOM 6 N1 DME A 999 1.909 69.504 68.623 -0.43 +0.06 -0.079
2.300
ATOM 7 C13 DME A 999 1.246 68.325 69.244 -0.26 -0.25 +0.271
2.300
ATOM 8 C14 DME A 999 1.316 70.688 69.280 -0.33 -0.31 +0.271
2.300
ATOM 9 C15 DME A 999 1.590 69.600 67.176 -0.25 -0.16 +0.271
2.300
ATOM 10 C7 DME A 999 4.998 64.535 70.028 -0.68 -0.00 +0.000
2.300
ATOM 11 C8 DME A 999 3.596 64.183 70.549 -0.47 -0.00 +0.000
2.300
ATOM 12 C9 DME A 999 2.531 65.179 70.006 -0.44 -0.00 +0.002
2.300
ATOM 13 C10 DME A 999 1.228 65.269 70.843 -0.44 -0.02 +0.028
2.300
ATOM 14 C11 DME A 999 0.797 64.009 71.641 -0.25 -0.15 +0.236
2.300
ATOM 15 N12 DME A 999 0.020 63.001 70.845 -0.37 +0.04 -0.079
2.300
ATOM 16 C16 DME A 999 0.900 61.882 70.421 -0.25 -0.11 +0.271
2.300
ATOM 17 C17 DME A 999 -0.581 63.637 69.662 -0.32 -0.14 +0.271
2.300
ATOM 18 C18 DME A 999 -1.112 62.489 71.627 -0.31 -0.15 +0.271
2.300
TER
ENDMDL
MODEL 6
USER Run = 6
USER Cluster Rank = 4
USER Number of conformations in this cluster = 2
USER
USER RMSD from reference structure = 2.293 A
USER
USER Estimated Free Energy of Binding = -5.84 kcal/mol
[=(1)+(2)+(3)-(4)]
USER Estimated Inhibition Constant, Ki = 52.57 uM (micromolar)
[Temperature = 298.15 K]
USER
USER (1) Final Intermolecular Energy = -8.97 kcal/mol
USER vdW + Hbond + desolv Energy = -7.91 kcal/mol
USER Electrostatic Energy = -1.07 kcal/mol
USER (2) Final Total Internal Energy = -0.45 kcal/mol
USER (3) Torsional Free Energy = +3.28 kcal/mol
USER (4) Unbound System's Energy = -0.31 kcal/mol
USER
USER
USER
USER DPF = DME.dpf
USER NEWDPF move DME.pdbqt
USER NEWDPF about 3.138400 65.846900 67.782300
USER NEWDPF tran0 6.657537 64.393433 68.962612
USER NEWDPF axisangle0 -0.251003 -0.706244 0.661980 -126.195399
USER NEWDPF quaternion0 -0.223839 -0.629814 0.590340 -0.452471
USER NEWDPF dihe0 -51.40 173.31 102.51 51.17 -48.06 -44.56 -24.20 -145.80
158.82 27.75 57.53
USER
USER x y z vdW Elec q
RMS
ATOM 1 C6 DME A 999 4.900 65.251 69.974 -0.68 -0.00 +0.000
2.293
ATOM 2 C5 DME A 999 4.931 63.729 70.024 -0.60 -0.00 +0.000
2.293
ATOM 3 C4 DME A 999 3.774 63.016 69.294 -0.50 -0.00 +0.002
2.293
ATOM 4 C3 DME A 999 4.268 61.597 69.014 -0.52 -0.01 +0.028
2.293
ATOM 5 C2 DME A 999 3.332 60.412 69.285 -0.40 -0.06 +0.236
2.293
ATOM 6 N1 DME A 999 3.688 59.796 70.579 -0.39 +0.02 -0.079
2.293
ATOM 7 C13 DME A 999 4.916 60.400 71.165 -0.37 -0.04 +0.271
2.293
ATOM 8 C14 DME A 999 2.617 60.026 71.571 -0.17 -0.09 +0.271
2.293
ATOM 9 C15 DME A 999 3.833 58.327 70.422 -0.43 -0.07 +0.271
2.293
ATOM 10 C7 DME A 999 5.716 65.843 68.850 -0.69 -0.00 +0.000
2.293
ATOM 11 C8 DME A 999 5.019 66.797 67.868 -0.55 -0.00 +0.000
2.293
ATOM 12 C9 DME A 999 5.407 66.467 66.397 -0.51 -0.00 +0.002
2.293
ATOM 13 C10 DME A 999 4.776 67.397 65.326 -0.39 -0.01 +0.028
2.293
ATOM 14 C11 DME A 999 5.645 67.770 64.096 -0.26 -0.15 +0.236
2.293
ATOM 15 N12 DME A 999 5.346 69.118 63.506 -0.45 +0.06 -0.079
2.293
ATOM 16 C16 DME A 999 6.290 70.137 64.031 -0.37 -0.23 +0.271
2.293
ATOM 17 C17 DME A 999 3.963 69.515 63.814 -0.27 -0.16 +0.271
2.293
ATOM 18 C18 DME A 999 5.417 69.065 62.041 -0.35 -0.32 +0.271
2.293
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=18 # atoms
AVSFLD: dim2=4 # 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 = DME.dlg.pdb filetype = ascii offset = 5 stride = 12
AVSFLD: variable 2 file = DME.dlg.pdb filetype = ascii offset = 6 stride = 12
AVSFLD: variable 3 file = DME.dlg.pdb filetype = ascii offset = 7 stride = 12
AVSFLD: variable 4 file = DME.dlg.pdb filetype = ascii offset = 8 stride = 12
AVSFLD: variable 5 file = DME.dlg.pdb filetype = ascii offset = 9 stride = 12
AVSFLD: variable 6 file = DME.dlg.pdb filetype = ascii offset = 10 stride = 12
AVSFLD: variable 7 file = DME.dlg.pdb filetype = ascii offset = 11 stride = 12
AVSFLD: # end of file
>>> Closing the docking parameter file (DPF)...
This docking finished at: 9:20 12" a.m., 06/05/2018
________________________________________________________________________________
/home/comp/Apps/Autodock/autodock4: Successful Completion on "AbNormal"
Real= 3m 07.64s, CPU= 3m 07.54s, System= 0.02s
________________________________________________________________________________
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