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Template of dock6.9 for GBSA Hawkins rescore of docked molecules. Replace LIG with your mol2 file of docked ligands and REC by your mol2 file for the receptor
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| conformer_search_type flex | |
| write_fragment_libraries no | |
| 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 | |
| pruning_conformer_score_scaling_factor 1.0 | |
| use_clash_overlap no | |
| write_growth_tree no | |
| use_internal_energy no | |
| ligand_atom_file LIG | |
| limit_max_ligands no | |
| skip_molecule no | |
| read_mol_solvation no | |
| calculate_rmsd no | |
| use_database_filter no | |
| orient_ligand no | |
| bump_filter no | |
| score_molecules yes | |
| contact_score_primary no | |
| contact_score_secondary no | |
| grid_score_primary no | |
| grid_score_secondary no | |
| multigrid_score_primary no | |
| multigrid_score_secondary no | |
| dock3.5_score_primary no | |
| dock3.5_score_secondary no | |
| continuous_score_primary no | |
| continuous_score_secondary no | |
| footprint_similarity_score_primary no | |
| footprint_similarity_score_secondary no | |
| pharmacophore_score_primary no | |
| pharmacophore_score_secondary no | |
| descriptor_score_primary no | |
| descriptor_score_secondary no | |
| gbsa_zou_score_primary no | |
| gbsa_zou_score_secondary no | |
| gbsa_hawkins_score_primary yes | |
| gbsa_hawkins_score_secondary yes | |
| gbsa_hawkins_score_rec_filename REC | |
| gbsa_hawkins_score_solvent_dielectric 78.5 | |
| gbsa_hawkins_use_salt_screen yes | |
| gbsa_hawkins_score_salt_conc(M) 0.15 | |
| gbsa_hawkins_score_gb_offset 0.09 | |
| gbsa_hawkins_score_cont_vdw_and_es yes | |
| gbsa_hawkins_score_vdw_att_exp 6 | |
| gbsa_hawkins_score_vdw_rep_exp 9 | |
| grid_score_rep_rad_scale 1 | |
| minimize_ligand no | |
| atom_model all | |
| vdw_defn_file /path_to/dock6/parameters/vdw_AMBER_parm99.defn | |
| flex_defn_file /path_to/dock6/parameters/flex.defn | |
| flex_drive_file /path_to/dock6/parameters/flex_drive.tbl | |
| ligand_outfile_prefix RESULTSPREFIX | |
| write_orientations no | |
| num_primary_scored_conformers_rescored 1 | |
| num_secondary_scored_conformers 1 | |
| rank_primary_ligands no | |
| rank_secondary_ligands no |
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