[Dock-fans] missing entries after GB/SA rescoring

Terry Lang terry at cgl.ucsf.edu
Thu Oct 6 19:58:54 PDT 2005


Dear RyangGuk,

          There is an internal energy score cutoff, but that is only 
applied during flexible ligand docking.  For this run, though, it 
appears that DOCK is only seeing six of the seven molecules, which is 
what it is scoring.  Are you sure all seven molecules were successfully 
docked originally?  Did you get any errors in the original docking 
output file?

Sincerely,
Terry


RyangGuk Kim wrote:

>dear terry,
>
>no... there was not any error message. below is the output of my dock_db_gbsa.out:
>
>--------------------------------------
>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                                             fk506ligands_out_scored.mol2
>ligand_outfile_prefix                                        fk506ligands_out_scored_gbsa
>limit_max_ligands                                            no
>write_orientations                                           no
>write_conformations                                          no
>initial_skip                                                 0
>calculate_rmsd                                               no
>rank_ligands                                                 no
>num_scored_poses_written                                     1
>
>Orient Ligand Parameters
>------------------------------------------------------------------------------------------
>orient_ligand                                                no
>
>Flexible Ligand Parameters
>------------------------------------------------------------------------------------------
>flexible_ligand                                              no
>
>Bump Filter Parameters
>------------------------------------------------------------------------------------------
>bump_filter                                                  no
>
>Master Score Parameters
>------------------------------------------------------------------------------------------
>score_molecules                                              yes
>
>Energy Score Parameters
>------------------------------------------------------------------------------------------
>energy_score_primary                                         no
>energy_score_secondary                                       no
>
>Continuous Energy Score Parameters
>------------------------------------------------------------------------------------------
>continuous_energy_score_primary                              no
>continuous_energy_score_secondary                            no
>
>Contact Score Paramters
>------------------------------------------------------------------------------------------
>contact_score_primary                                        no
>contact_score_secondary                                      no
>
>GB/SA Score Parameters
>------------------------------------------------------------------------------------------
>gbsa_pairwise_score_primary                                  yes
>gbsa_pairwise_score_secondary                                yes
>gbsa_pairwise_gb_grid_prefix                                 GB_grids/GB_grid
>gbsa_pairwise_sa_grid_prefix                                 SA_grids/SA_grid
>gbsa_pairwise_screen_file                                    /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/screen.in
>gbsa_pairwise_solvent_dielectric                             78.300003
>gbsa_pairwise_vdw_grid_prefix                                grid
>
>Simplex Minimization Parameters
>------------------------------------------------------------------------------------------
>minimize_ligand                                              no
>
>Atom Typing Parameters
>------------------------------------------------------------------------------------------
>atom_model                                                   all
>vdw_defn_file                                                /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/vdw_AMBER_parm99.defn
>flex_defn_file                                               /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/flex.defn
>flex_drive_file                                              /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/flex_drive.tbl
>chem_defn_file                                               /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/chem.defn
>------------------------------------------------------------------------------------------
>
>Initializing Library File Routines...
>Initializing GB/SA Pairwise Score Routines...
>Initializing Energy Score Routines...
> Reading the energy grid from grid.nrg
>
>-----------------------------------
>Molecule: 1d7i_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:             3.959651
>         vdw:           -16.553610
>          gb:            15.122217
>          sa:          -398.240021
>  del_SAS_hp:          -288.160034
>
>
>-----------------------------------
>Molecule: 1d7j_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:             5.203935
>         vdw:           -17.197752
>          gb:            15.073786
>          sa:          -326.720032
>  del_SAS_hp:          -178.080017
>
>
>-----------------------------------
>Molecule: 1fkb_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:            30.429562
>         vdw:           -42.310616
>          gb:            54.779930
>          sa:          -981.600037
>  del_SAS_hp:          -547.520020
>
>
>-----------------------------------
>Molecule: 1fkg_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:            13.776014
>         vdw:           -40.599159
>          gb:            34.908310
>          sa:          -733.280029
>  del_SAS_hp:          -310.880035
>
>
>-----------------------------------
>Molecule: 1fkh_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:            16.251358
>         vdw:           -40.126366
>          gb:            37.895977
>          sa:          -665.280029
>  del_SAS_hp:          -301.920013
>
>
>-----------------------------------
>Molecule: 1fki_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:            24.895756
>         vdw:           -18.204834
>          gb:            34.138657
>          sa:          -497.600037
>  del_SAS_hp:          -231.360016
>
>
>
>6 Molecules Processed
>Elapsed time:   0.98 seconds
>
>---------------------
>
>the receptor was a partially unfolded form of the ligands' original receptor. the dock_db_gbsa.out for the native form of the receptor was as follows:
>
>--------------------------------------
>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                                             fk506ligands_out_scored.mol2
>ligand_outfile_prefix                                        fk506ligands_1fkg_0_gbsa
>limit_max_ligands                                            no
>write_orientations                                           no
>write_conformations                                          no
>initial_skip                                                 0
>calculate_rmsd                                               no
>rank_ligands                                                 no
>num_scored_poses_written                                     1
>
>Orient Ligand Parameters
>------------------------------------------------------------------------------------------
>orient_ligand                                                no
>
>Flexible Ligand Parameters
>------------------------------------------------------------------------------------------
>flexible_ligand                                              no
>
>Bump Filter Parameters
>------------------------------------------------------------------------------------------
>bump_filter                                                  no
>
>Master Score Parameters
>------------------------------------------------------------------------------------------
>score_molecules                                              yes
>
>Energy Score Parameters
>------------------------------------------------------------------------------------------
>energy_score_primary                                         no
>energy_score_secondary                                       no
>
>Continuous Energy Score Parameters
>------------------------------------------------------------------------------------------
>continuous_energy_score_primary                              no
>continuous_energy_score_secondary                            no
>
>Contact Score Paramters
>------------------------------------------------------------------------------------------
>contact_score_primary                                        no
>contact_score_secondary                                      no
>
>GB/SA Score Parameters
>------------------------------------------------------------------------------------------
>gbsa_pairwise_score_primary                                  yes
>gbsa_pairwise_score_secondary                                yes
>gbsa_pairwise_gb_grid_prefix                                 GB_grids/gb_grid
>gbsa_pairwise_sa_grid_prefix                                 SA_grids/sa_grid
>gbsa_pairwise_screen_file                                    /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/screen.in
>gbsa_pairwise_solvent_dielectric                             78.300003
>gbsa_pairwise_vdw_grid_prefix                                grid
>
>Simplex Minimization Parameters
>------------------------------------------------------------------------------------------
>minimize_ligand                                              no
>
>Atom Typing Parameters
>------------------------------------------------------------------------------------------
>atom_model                                                   all
>vdw_defn_file                                                /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/vdw_AMBER_parm99.defn
>flex_defn_file                                               /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/flex.defn
>flex_drive_file                                              /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/flex_drive.tbl
>chem_defn_file                                               /net/dell/10/ryangguk/DOCK/dock.5.2_linux/parameters/chem.defn
>------------------------------------------------------------------------------------------
>
>Initializing Library File Routines...
>Initializing GB/SA Pairwise Score Routines...
>Initializing Energy Score Routines...
> Reading the energy grid from grid.nrg
>
>-----------------------------------
>Molecule: 1d7i_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:             3.989157
>         vdw:           -15.451047
>          gb:            14.529385
>          sa:          -402.560028
>  del_SAS_hp:          -292.320007
>
>
>-----------------------------------
>Molecule: 1d7j_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:             7.016787
>         vdw:           -15.006313
>          gb:            15.442974
>          sa:          -341.440033
>  del_SAS_hp:          -181.760010
>
>
>-----------------------------------
>Molecule: 1fkb_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:            18.884865
>         vdw:           -41.651794
>          gb:            42.867142
>          sa:         -1037.119995
>  del_SAS_hp:          -581.920044
>
>Pure ligand inv_a error: 123    -21.4973
>Pure ligand inv_a error: 124    -21.3578
>Pure ligand inv_a error: 125    -21.3591
>Receptor on ligand inv_a error: 123     -21.5188
>Receptor on ligand inv_a error: 124     -21.3825
>Receptor on ligand inv_a error: 125     -21.3665
>
>-----------------------------------
>Molecule: 1fkf_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:            24.422497
>         vdw:           -36.374599
>          gb:            44.420856
>          sa:          -822.560059
>  del_SAS_hp:          -420.480042
>
>
>-----------------------------------
>Molecule: 1fkg_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:            20.617302
>         vdw:           -45.508865
>          gb:            43.747421
>          sa:          -762.080017
>  del_SAS_hp:          -290.240021
>
>
>-----------------------------------
>Molecule: 1fkh_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:            16.902935
>         vdw:           -44.408119
>          gb:            39.975006
>          sa:          -670.720032
>  del_SAS_hp:          -259.520020
>
>
>-----------------------------------
>Molecule: 1fki_ligand
>
> Anchors:               1
> Orientations:          1
> Conformations:         1
>
> GB/SA Score:             7.889725
>         vdw:           -22.455212
>          gb:            19.782852
>          sa:          -389.600006
>  del_SAS_hp:          -170.560013
>
>
>
>7 Molecules Processed
>Elapsed time:   0.68 seconds
>
>--------------------------------
>
>an interesting thing is, when i tried Glide from Schrodinger some ligands couldn't produce docked structures with partially unfolded receptor structures due to their failing one or more of Glide's criteria for computing GScore. is there any 'deleting' algorithm in DOCK for ligands with irresolvable steric clash (missed ligands were all big)?
>
>sincerely,
>ryangguk
>
>
> 
>Terry Lang <terry at cgl.ucsf.edu> wrote the Oct 6, 2005 4:54 PM:
>
>  
>
>>Dear RyangGuk,
>>
>>       Did you get any error messages in your out file in regards to the 
>>missing ligands?
>>
>>Sincerely,
>>Terry
>>
>>
>>RyangGuk Kim wrote:
>>
>>    
>>
>>>hi, i'm new to DOCK and now trying GB/SA rescoring with it. i have found that sometimes several ligands are omitted after GB/SA rescoring. for example, i used an unfolded structure of a receptor, A, and ligands 1 to 7. i could dock A and 1 to 7 all successfully. then i rescored with GB/SA according to the introductory tutorial and found that ligands 3 and 4 were missing in the out file. does anyone know the reason for this? thank you very much. :)
>>>
>>>
>>>_______________________________________________
>>>Dock-fans mailing list
>>>Dock-fans at docking.org
>>>http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>>> 
>>>
>>>      
>>>
>>-- 
>>P. Therese Lang
>>Kuntz and James Labs
>>UCSF--Chemistry and Chemical Biology
>>Phone: (415)476-3986
>>
>> 
>>
>>
>>    
>>
>
>
>  
>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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