[Dock-fans] error happened when I ran felxiable dock ing

鹿晶jinger.Lu lujing1999 at 126.com
Wed Dec 5 23:10:41 PST 2007


Hi, dock-fans, 
 I am trying to dock  a set of ligands using flexible ligand docking. I used the file  tutorial /mpi_demo/4_dock/mpi.in as the template .  Using sphere_slector, I selected the sphere within 6.0Ang of the ligand. with the generated .sph file , I created a box using showbox with extra margin of 5A. After running dock6.mpi , the job gave the following output :
Molecule: Palmitoyl glycine
 Elapsed time:  2 seconds
 ERROR:  Could not complete growth. 
         Confirm grid box is large enough to contain 
         ligand and try increasing max_orients.
there are 60 molecule in my set, and 41  are showed errors like that.  I also ran serial dock with the same parameter file, and the same 41 ligands showed same errors. I also tried a single molecule , and got the same error message. Otherwise, I tried rigid docking also using the same ligands set, and no errors showed.  
the following is the output file when I tried a single molecule . please let me know if I am missing something here. thanks for your help
 
--------------------------------------
DOCK v6.1
Released December 2006
Copyright UCSF
--------------------------------------

Molecule Library Input Parameters
------------------------------------------------------------------------------------------
ligand_atom_file                                             test.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
Orient Ligand Parameters
------------------------------------------------------------------------------------------
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ../2_site/rec.sph
max_orientations                                             500
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
Flexible Ligand Parameters
------------------------------------------------------------------------------------------
flexible_ligand                                              yes
min_anchor_size                                              40
pruning_use_clustering                                       yes
pruning_max_orients                                          100
pruning_clustering_cutoff                                    100
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                                                  no
Master Score Parameters
------------------------------------------------------------------------------------------
score_molecules                                              yes
Contact Score Paramters
------------------------------------------------------------------------------------------
contact_score_primary                                        no
contact_score_secondary                                      no
Grid Score Parameters
------------------------------------------------------------------------------------------
grid_score_primary                                           yes
grid_score_secondary                                         no
grid_score_rep_rad_scale                                     1
grid_score_vdw_scale                                         1
grid_score_es_scale                                          1
grid_score_grid_prefix                                       ../3_grid/grid
Dock3.5 Score Parameters
------------------------------------------------------------------------------------------
dock3.5_score_secondary                                      no
Continuous Energy Score Parameters
------------------------------------------------------------------------------------------
continuous_score_secondary                                   no
Zou GB/SA Score Parameters
------------------------------------------------------------------------------------------
gbsa_zou_score_secondary                                     no
Hawkins GB/SA Score Parameters
------------------------------------------------------------------------------------------
gbsa_hawkins_score_secondary                                 no
Amber Score Parameters
------------------------------------------------------------------------------------------
amber_score_secondary                                        no
Warning:  No secondary scoring function selected.

Simplex Minimization Parameters
------------------------------------------------------------------------------------------
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
use_advanced_simplex_parameters                              no
simplex_max_cycles                                           1
simplex_score_converge                                       0.1
simplex_cycle_converge                                       1.0
simplex_trans_step                                           1.0
simplex_rot_step                                             0.1
simplex_tors_step                                            10.0
simplex_anchor_max_iterations                                500
simplex_grow_max_iterations                                  500
simplex_final_min                                            no
simplex_random_seed                                          0
Atom Typing Parameters
------------------------------------------------------------------------------------------
atom_model                                                   all
vdw_defn_file                                                ../../parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               ../../parameters/flex.defn
flex_drive_file                                              ../../parameters/flex_drive.tbl
Molecule Library Output Parameters
------------------------------------------------------------------------------------------
ligand_outfile_prefix                                        1G3J_2801
write_orientations                                           no
num_scored_conformers_written                                1
rank_ligands                                                 no
------------------------------------------------------------------------------------------
Initializing Library File Routines...
Initializing Orienting Routines...
Initializing Conformer Generator Routines...
Initializing Grid Score Routines...
 Reading the energy grid from ../3_grid/grid.nrg
-----------------------------------
Molecule: Docosahexaenoyl ethanolamide
 Elapsed time:  3 seconds
 ERROR:  Could not complete growth. 
         Confirm grid box is large enough to contain 
         ligand and try increasing max_orients.


 
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