Joe and Brian de novo stuff

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This is our secret wiki page.

This is the version of the code on cluster that we should be using

/sbhome1/wjallen/work/build/dock.6.7_2015-02-17.denovo_paper

/sbhome1/wjallen/work/build/dock.6.7_2015-02-17.denovo_paper/src/dock/dock6


This is the input file we should be using 

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     ../002.generate-frags/fraglib_scaffold.mol2
dn_fraglib_linker_file                                       ../002.generate-frags/fraglib_linker.mol2
dn_fraglib_sidechain_file                                    ../002.generate-frags/fraglib_sidechain.mol2
dn_user_specified_anchor                                     no
dn_use_torenv_table                                          yes

dn_torenv_table ../002.generate-frags/fraglib_torenv.dat dn_sampling_method ex dn_pruning_conformer_score_cutoff 200.0 dn_torsion_rmsd_cutoff 0.5 dn_constraint_mol_wt 800 dn_constraint_rot_bon 12 dn_constraint_formal_charge 2.0 dn_constraint_charge_groups 6 dn_tanimoto_cutoff 0.8 dn_heur_unmatched_num 2 dn_heur_matched_rmsd 2.0 dn_max_grow_layers 7 dn_max_current_aps 7 dn_max_root_size 40 dn_max_layer_size 40 dn_write_checkpoints no dn_write_orients no dn_write_growth_trees no dn_output_prefix final use_internal_energy yes internal_energy_rep_exp 12 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../001.files/1FPU.rec.clust.close.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres 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 ph4_score_primary no ph4_score_secondary no descriptor_score_primary yes descriptor_score_secondary no descriptor_use_grid_score yes descriptor_use_pharmacophore_score no descriptor_use_tanimoto yes descriptor_use_hungarian yes descriptor_grid_score_rep_rad_scale 1 descriptor_grid_score_vdw_scale 1 descriptor_grid_score_es_scale 1 descriptor_grid_score_grid_prefix ../001.files/1FPU.rec descriptor_fingerprint_ref_filename ../001.files/1FPU.lig.am1bcc.mol2 descriptor_hungarian_ref_filename ../001.files/1FPU.lig.am1bcc.mol2 descriptor_hungarian_matching_coeff -5 descriptor_hungarian_rmsd_coeff 1 descriptor_weight_grid_score 1 descriptor_weight_fingerprint_tanimoto 0 descriptor_weight_hungarian 0 gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_descriptor_score_secondary no amber_score_secondary no minimize_ligand yes minimize_anchor yes minimize_flexible_growth yes use_advanced_simplex_parameters no simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0 simplex_rot_step 0.1 simplex_tors_step 10.0 simplex_anchor_max_iterations 500 simplex_grow_max_iterations 20 simplex_grow_tors_premin_iterations 0 simplex_random_seed 0 simplex_restraint_min yes simplex_coefficient_restraint 10 atom_model all vdw_defn_file ../zzz.dock-files/vdw_AMBER_parm99.defn flex_defn_file ../zzz.dock-files/flex.defn flex_drive_file ../zzz.dock-files/flex_drive.tbl

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