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

RyangGuk Kim RyangGuk.Kim at bioinformatics.buffalo.edu
Thu Oct 6 14:48:14 PDT 2005


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
> 
>  
> 
>





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