[Dock-fans] Could Not Complete Growth Error

Trent E. Balius tbalius at aol.com
Tue Nov 27 12:19:05 PST 2012


 Hi Austin,

This is definitely an orienting problem.  I would do as Joe suggests and visualizes your spheres, protein, grid, gird box etc. in chimera and verify that they are as you expect.   

See the following tutorial and the section on Surface and Spheres generation: 
http://ringo.ams.sunysb.edu/index.php/2012_DOCK_tutorial_with_Streptavidin#III._Generating_Receptor_Surface_and_Spheres

 

I hope this helps,

Trent

 

 

-----Original Message-----
From: Austin Baker <asb93 at pitt.edu>
To: Trent E. Balius <tbalius at aol.com>
Sent: Tue, Nov 27, 2012 11:35 am
Subject: Re: [Dock-fans] Could Not Complete Growth Error


Here is the dock.in file as run for benzoic acid. Also I tried running in verbose and got nothing of interest (see below). Also with this I am not getting any output files. Running in verbose created an output_ranked.mol2 file that contained no data.


Verbose output

VERBOSE MOLECULE STATS


  Number of heavy atoms = 9
  Number of rotatable bonds = 1
  Formal Charge = -1.00
  Molecular Weight = 121.12
  Heavy Atoms = 9
Orienting 7 anchor heavy atom centers



dock.in 

ligand_atom_file                                             zinc_1011.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       no
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           cSRC_spheres.sph
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
flexible_ligand                                              yes
user_specified_anchor                                        no
limit_max_anchors                                            no
min_anchor_size                                              5
pruning_use_clustering                                       yes
pruning_max_orients                                          1000
pruning_clustering_cutoff                                    100
pruning_conformer_score_cutoff                               100.0
use_clash_overlap                                            no
write_growth_tree                                            no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
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                                       grid
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
amber_score_secondary                                        no
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_grow_tors_premin_iterations                          0
simplex_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /Applications/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /Applications/dock6/parameters/flex.defn
flex_drive_file                                              /Applications/dock6/parameters/flex_drive.tbl
ligand_outfile_prefix                                        cSRC.output
write_orientations                                           no
num_scored_conformers                                        5000
write_conformations                                          no
cluster_conformations                                        yes
cluster_rmsd_threshold                                       0.2
rank_ligands                                                 yes
max_ranked_ligands                                           100













Austin Baker
asb93 at pitt.edu
Graduate Student
Department of Chemistry
University of Pittsburgh


Everything is Experimental







On Nov 27, 2012, at 1:43 PM, "Trent E. Balius" <tbalius at aol.com> wrote:


 Hi,

You might also try runing dock with the verbose flag.  This might help isolate where dock is encountering problems.  

See the following:
http://mailman.docking.org/pipermail/dock-fans/2010-June/002392.html


Trent
 

-----Original Message-----
From: William Joseph Allen <william.joseph.allen at gmail.com>
To: Austin Baker <asb93 at pitt.edu>
Cc: dock-fans <dock-fans at docking.org>
Sent: Tue, Nov 27, 2012 10:37 am
Subject: Re: [Dock-fans] Could Not Complete Growth Error


Hi Austin,

How are you orienting the ligands? I assume you are using automated_matching = yes? If so, what is your sphere input file that you specify in the parameter file? If you open up the spheres in Chimera, do they fall where you expect with respect to your protein? If you also open up the box / grid, does it surround the spheres with a wide margin? Feel free to cut and paste the contents of your dock.in file so we can see whether there are any red flags.

Joe Allen





On Tue, Nov 27, 2012 at 1:23 PM, Austin Baker <asb93 at pitt.edu> wrote:

All,


	I am new to Dock and am having trouble running through the tutorials with my protein of interest. Thanks for the patience and help in advance.


	Every time that I try and dock a ligand I keep getting the same error message of:

 ERROR:  Could not complete growth.
         Confirm that the grid box is large enough to contain the ligand,
         and try increasing max_orientations.


I have tried searching through the archives and so far none of the options that are listed have helped. I have tried to increase the size of the box manually to a 30x30x30 box, increase the max conformers, played with the bump filter, the internal energy and use of the flexible ligand. In addition I have tried to dock something small like benzoic acid and cyclohexene but keep getting the same error messages.



Very much appreciated



Austin Baker
asb93 at pitt.edu
Graduate Student
Department of Chemistry
University of Pittsburgh


Everything is Experimental








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-- 
William Joseph Allen, Ph.D.
Robert C. Rizzo Research Group
Department of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/


 
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