-------------------------------------- DOCK v6.5 Released July 2011 Copyright UCSF -------------------------------------- Molecule Library Input Parameters ------------------------------------------------------------------------------------------ ligand_atom_file lig.amber_score.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no Database Filter Parameters ------------------------------------------------------------------------------------------ use_database_filter no Orient Ligand Parameters ------------------------------------------------------------------------------------------ orient_ligand no Internal Energy Parameters ------------------------------------------------------------------------------------------ use_internal_energy no Flexible Ligand Parameters ------------------------------------------------------------------------------------------ flexible_ligand no Bump Filter Parameters ------------------------------------------------------------------------------------------ bump_filter no Master Score Parameters ------------------------------------------------------------------------------------------ score_molecules yes Contact Score Parameters ------------------------------------------------------------------------------------------ contact_score_primary no contact_score_secondary no Grid Score Parameters ------------------------------------------------------------------------------------------ grid_score_primary no grid_score_secondary no Dock3.5 Score Parameters ------------------------------------------------------------------------------------------ dock3.5_score_primary no dock3.5_score_secondary no Continuous Energy Score Parameters ------------------------------------------------------------------------------------------ continuous_score_primary no continuous_score_secondary no Descriptor Energy Score Parameters ------------------------------------------------------------------------------------------ descriptor_score_primary no descriptor_score_secondary no Zou GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_zou_score_primary no gbsa_zou_score_secondary no Hawkins GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes amber_score_secondary no amber_score_receptor_file_prefix 1lgu amber_score_movable_region ligand amber_score_minimization_rmsgrad 0.01 amber_score_before_md_minimization_cycles 100 amber_score_md_steps 3000 amber_score_after_md_minimization_cycles 100 amber_score_gb_model 5 amber_score_nonbonded_cutoff 18.0 amber_score_temperature 300.0 amber_score_abort_on_unprepped_ligand yes Warning: No secondary scoring function selected. Molecule Library Output Parameters ------------------------------------------------------------------------------------------ ligand_outfile_prefix output write_orientations no num_scored_conformers 1 rank_ligands no ------------------------------------------------------------------------------------------ Initializing Library File Routines... ----------------------------------- Molecule: AAH Elapsed time for docking: 28 seconds Anchors: 1 Orientations: 1 Conformations: 1 Amber Score: -4.230798 complex: -4657.737211 receptor: 4584.941716 ligand: 68.564696 1 Molecules Processed Total elapsed time: 30 seconds