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zmywahrheit金蟲 (初入文壇)
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[求助]
DOCK里面說盒子小的原因是什么？
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日志文件： -------------------------------------- DOCK v6.4 Released May 2010 Copyright UCSF -------------------------------------- Molecule Library Input Parameters ------------------------------------------------------------------------------------------ ligand_atom_file ligand.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename ligand_rmsd.mol2 Database Filter Parameters ------------------------------------------------------------------------------------------ use_database_filter no Orient Ligand Parameters ------------------------------------------------------------------------------------------ orient_ligand yes automated_matching yes receptor_site_file rec.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres no Internal Energy Parameters ------------------------------------------------------------------------------------------ use_internal_energy yes internal_energy_rep_exp 12 Note: Internal energy only includes repulsive VDW for growth and/or minimization. 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 yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix grid Dock3.5 Score Parameters ------------------------------------------------------------------------------------------ dock3.5_score_secondary no Continuous Energy Score Parameters ------------------------------------------------------------------------------------------ continuous_score_secondary no Zou GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_zou_score_secondary no Hawkins GB/SA Score Parameters ------------------------------------------------------------------------------------------ gbsa_hawkins_score_secondary no Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_secondary no Warning: No secondary scoring function selected. Simplex Minimization Parameters ------------------------------------------------------------------------------------------ minimize_ligand yes simplex_max_iterations 1000 simplex_tors_premin_iterations 0 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_random_seed 0 simplex_restraint_min no Atom Typing Parameters ------------------------------------------------------------------------------------------ atom_model all vdw_defn_file vdw_AMBER_parm99.defn flex_defn_file flex.defn flex_drive_file flex_drive.tbl Molecule Library Output Parameters ------------------------------------------------------------------------------------------ ligand_outfile_prefix rigid write_orientations no num_scored_conformers 1 rank_ligands no ------------------------------------------------------------------------------------------ Initializing Library File Routines... Initializing Orienting Routines... Initializing Grid Score Routines... Reading the energy grid from grid.nrg Done reading the energy grid. ----------------------------------- Molecule: ligand.pdb Elapsed time: 1 seconds ERROR: Could not complete growth. Confirm that the grid box is large enough to contain the ligand, and try increasing max_orientations. 盒子已經(jīng)足夠大了 |
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