[Dock-fans] Missing Scores [signed]

M. A. Lardy [c] lardy at chemistry.ucsc.edu
Wed Apr 6 16:06:43 PDT 2005


Hi all,

I am having difficulty getting the scores out of docking runs.  I am  
running Dock v5.2.0, and this is what I see from the run:


--------------------------------------
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                                              
23ligands.mol2
ligand_outfile_prefix                                        sertanty
limit_max_ligands                                            no
write_orientations                                           yes
write_conformations                                          yes
initial_skip                                                 0
calculate_rmsd                                               yes
use_rmsd_reference_mol                                        
23ligands.mol2
rank_ligands                                                 yes
max_ranked_ligands                                           500
scored_mol_output_override                                   no

Orient Ligand Parameters
------------------------------------------------------------------------ 
------------------
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                            
/home/lardy/research2/ucn01pocket/1nvqunbound.sph
max_orientations                                             1000
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                                              50
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                                                    2

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                                              yes
minimize_flexible_growth                                     yes
minimize_final_pose                                          yes
use_advanced_simplex_parameters                              yes
simplex_anchor_min_max_iterations                            50
simplex_anchor_min_max_cycles                                1
simplex_anchor_min_score_converge                            0.1
simplex_anchor_min_cycle_converge                            1.0
simplex_anchor_min_trans_step                                1.0
simplex_anchor_min_rot_step                                  0.1
simplex_anchor_min_tors_step                                 10.0
simplex_flex_min_max_iterations                              10
simplex_flex_min_max_cycles                                  1
simplex_flex_min_score_converge                              0.1
simplex_flex_min_cycle_converge                              1.0
simplex_flex_min_trans_step                                  1.0
simplex_flex_min_rot_step                                    0.1
simplex_flex_min_tors_step                                   10.0
simplex_final_min_max_iterations                             100
simplex_final_min_max_cycles                                 1
simplex_final_min_score_converge                             0.1
simplex_final_min_cycle_converge                             1.0
simplex_final_min_trans_step                                 1.0
simplex_final_min_rot_step                                   0.1
simplex_final_min_tors_step                                  10.0
simplex_random_seed                                          0

Atom Typing Parameters
------------------------------------------------------------------------ 
------------------
atom_model                                                   all
vdw_defn_file                                                 
/usr/local/software/dock/dock.5.2_linux/parameters/ 
vdw_AMBER_parm94.defn
flex_defn_file                                                
/usr/local/software/dock/dock.5.2_linux/parameters/flex.defn
flex_drive_file                                               
/usr/local/software/dock/dock.5.2_linux/parameters/flex_drive.tbl
chem_defn_file                                                
/usr/local/software/dock/dock.5.2_linux/parameters/chem.defn
------------------------------------------------------------------------ 
------------------

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


23 Molecules Processed
Elapsed time:	56.82 seconds

It appears to me that the run was successful, but when I open the  
sertanty prefix files, they are all empty with one exception.  The  
exception being that the sertanty_orient.mol2 has structures.  Am I  
missing something?  I am more than happy to share any other information  
that might be relevant to this problem.

Thanks,
Matthew


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