[Dock-fans] Rescore

[Scott Brozell]

Hi,

On Mon, 20 Oct 2008, Salvatore Bongarzone wrote:

> Is it possible to use a complex structure (ligand docked to the target) 
> as an input to DOCK6 and score its energy?
> In other words, we would like to rescore the binding energy of the 
> ligand without docking but starting straight from the rigid complex.

Yes, DOCK is frequently used for rescoring (although the initial
set is usually ligand conformations from previous DOCKing).
As a quick start here are two input files one for 
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ContinuousScore
and one for 
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
And follow tutorials
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm
and 
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm
respectively.

Scott

ligand_atom_file                                             lig_.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
orient_ligand                                                no
flexible_ligand                                              no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     yes
continuous_score_secondary                                   no
cont_score_rec_filename                                      rec.mol2
cont_score_att_exp                                           6
cont_score_rep_exp                                           12
cont_score_rep_rad_scale                                     1
use_distance_dependent_dielectric                            no
cont_score_dielectric                                        1.0
cont_score_vdw_scale                                         1
cont_score_es_scale                                          1
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
amber_score_secondary                                        no
minimize_ligand                                              no
atom_model                                                   all
vdw_defn_file                                                /home/scott/dock/uptodatedock6/parameters/vdw_AMBER_parm94.defn
flex_defn_file                                               /home/scott/dock/uptodatedock6/parameters/flex.defn
flex_drive_file                                              /home/scott/dock/uptodatedock6/parameters/flex_drive.tbl
ligand_outfile_prefix                                        output_
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no


ligand_atom_file                                             grid_charge_sampling_conformers.amber_score.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               yes
use_rmsd_reference_mol                                       lig_OPT.mol2
orient_ligand                                                no
flexible_ligand                                              no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     no
continuous_score_secondary                                   no
gbsa_zou_score_primary                                       no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_primary                                   no
gbsa_hawkins_score_secondary                                 no
amber_score_primary                                          yes
amber_score_secondary                                        no
amber_score_receptor_file_prefix                             rec
amber_score_movable_region                                   nothing
amber_score_gb_model                                         5
amber_score_nonbonded_cutoff                                 18.0
amber_score_temperature                                      300.0
amber_score_abort_on_unprepped_ligand                        no
atom_model                                                   all
vdw_defn_file                                                /home/scott/dock/uptodatedock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /home/scott/dock/uptodatedock6/parameters/flex.defn
flex_drive_file                                              /home/scott/dock/uptodatedock6/parameters/flex_drive.tbl
ligand_outfile_prefix                                        outputchargesampling
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no