[Dock-fans] Missing Scores [signed]

Terry Lang terry at cgl.ucsf.edu
Mon Apr 11 16:18:09 PDT 2005


Dear Matthew,

   Actually the 10000 value is default if some part of the ligand is 
hanging off the edge of the grid.  (We are also working on making that 
message more apparent in a bugfix to be released soon).  Before looking 
into the other suggestions on the list, make sure that your grid is large 
enough to accommodate both the spheres in your active site and your ligand(s).

Sincerely,
Terry


At 10:33 AM 4/11/2005, you wrote:
>Terry,
>
>Well after setting flexible_ligand to no, I do get scores for my
>compounds.  Although, they are all 10000 (that must be a default value
>for the maximum for sterical hindered binding scores).  The active site
>might be too constrained, but both the protein and three of ligands
>that I have been attempting to reposition are from crystal structure
>and have less than three rotatable bonds.  Anyway, I am going to try
>some of the suggestions that I have received from this list today, and
>let you all know what ended up working out.
>
>Thanks again,
>Matthew
>
>
>
>On Apr 7, 2005, at 3:48 PM, Terry Lang wrote:
>
>>Dear Matthew,
>>
>>   If you don't get a response at the end of your run, it is because,
>>for some reason, DOCK did not consider any of the generated poses to
>>have reasonable scores.  We know that it is confusing that nothing is
>>being printed out in the output file and are working to fix that, at
>>which point we will post a bugfix on the web page.
>>   For your particular case, because you do have orientations but do
>>not have conformations, you most likely did not get any scored poses
>>because anchor and grow could not find any conformations with
>>reasonable internal energies or reasonable interaction energies.  This
>>generally happens when a) your small molecule has > 7 rotatable bonds
>>or b) your active site is buried or in other ways very sterically
>>restricted.  In order to validate that the problem is actually the
>>flexible ligand sampling, you can perform a rigid dock run (set
>>"flexible_ligand" to no) and see if you get out answers.
>>   In order to deal with the sampling issue (if this is indeed the
>>problem), you can either try conformational expansion of your
>>ligand/library prior to docking and then keep your ligands rigid.  You
>>can also try to run either minimizations or md simulations of your
>>receptor-ligand complex to see if you can make your active site less
>>sterically restricted.
>>   Please let me know whether this solves your problem.
>>
>>Good luck,
>>Terry
>>
>>
>>At 04:06 PM 4/6/2005, M. A. Lardy [c] wrote:
>>>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
>>>
>>
>>>
>>>_______________________________________________
>>>Dock-fans mailing list
>>>Dock-fans at docking.org
>>>http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>>
>>***NOTE:  This is a new e-mail address (terry at cgl.ucsf.edu)  Please
>>update your address book!***
>>
>>P. Therese (Downing) Lang
>>Kuntz and James Labs
>>UCSF - CCB Graduate Program
>>Phone:  (415)476-3986
>>
>
>
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***NOTE:  This is a new e-mail address (terry at cgl.ucsf.edu)  Please update 
your address book!***

P. Therese (Downing) Lang
Kuntz and James Labs
UCSF - CCB Graduate Program
Phone:  (415)476-3986




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