[Dock-fans] Strange Energy Score~!

"이주용" nicole23 at naver.com
Mon Jul 18 00:01:08 PDT 2005


Skipped content of type multipart/alternative-------------- next part --------------



--------------------------------------
DOCK v5.2.0-Beta

Released March 2005
Copyright UCSF
Authored by:
	Tack Kuntz
	Demetri Moustakas
	Paula Therese Lang
	Scott Pegg
--------------------------------------


Molecule Library Parameters
------------------------------------------------------------------------------------------
ligand_atom_file                                             ./ligand/n1.mol2
ligand_outfile_prefix                                        ./n1-oldparameter/n1-oldparameter47
limit_max_ligands                                            no
write_orientations                                           no
write_conformations                                          yes
initial_skip                                                 0
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       no
rank_ligands                                                 no
num_scored_poses_written                                     1

Orient Ligand Parameters
------------------------------------------------------------------------------------------
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           selected_spheres.sph
max_orientations                                             100000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no

Flexible Ligand Parameters
------------------------------------------------------------------------------------------
flexible_ligand                                              yes

Anchor & Grow Parameters
------------------------------------------------------------------------------------------
ag_conf_search                                               yes
min_anchor_size                                              10
num_anchor_poses                                             50
number_confs_per_cycle                                       50
use_internal_energy                                          yes
internal_energy_att_exp                                      6
internal_energy_rep_exp                                      12
internal_energy_dielectric                                   4.0
use_clash_overlap                                            no

Bump Filter Parameters
------------------------------------------------------------------------------------------
bump_filter                                                  yes
bump_grid_prefix                                             grid
max_bumps                                                    0

Master Score Parameters
------------------------------------------------------------------------------------------
score_molecules                                              yes

Energy Score Parameters
------------------------------------------------------------------------------------------
energy_score_primary                                         yes
energy_score_secondary                                       yes
vdw_scale                                                    1
es_scale                                                     1
nrg_grid_prefix                                              grid

Simplex Minimization Parameters
------------------------------------------------------------------------------------------
minimize_ligand                                              yes
minimize_anchor                                              no
minimize_flexible_growth                                     yes
minimize_final_pose                                          yes
use_advanced_simplex_parameters                              no
simplex_max_cycles                                           10
simplex_score_converge                                       0.01
simplex_cycle_converge                                       1.0
simplex_trans_step                                           1.0
simplex_rot_step                                             0.1
simplex_tors_step                                            10.0
simplex_flex_min_max_iterations                              100
simplex_final_min_max_iterations                             1000
simplex_random_seed                                          47

Atom Typing Parameters
------------------------------------------------------------------------------------------
atom_model                                                   all
vdw_defn_file                                                ./vdw_AMBER_parm99.defn
flex_defn_file                                               ./flex.defn
flex_drive_file                                              ./flex_drive.tbl
chem_defn_file                                               ./chem.defn
------------------------------------------------------------------------------------------

Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Conformer Generator Routines...
Initializing Bump Filter Routines...
 Reading the bump grid from grid-marine-w.bmp
Initializing Energy Score Routines...
 Reading the energy grid from grid-marine-w.nrg

-----------------------------------
Molecule: 

 Anchors:		1
 Orientations:		3986
 Conformations:		32

 Energy Score:     -1194159.275211
          vdw:     -1194158.500000
           es:           -0.775211



1 Molecules Processed
Elapsed time:	972.27 seconds


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