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【求助】dock对接怎样显示结合位置？
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| 请教各位高手，我用DOCK6.0作分子对接，最后对接结果中只有一个dock.out文件，我想看一下配体是否在受体的活性位点上结合了，怎样才能得到能够显示配体与受体结合位点的文件？望高手指教，不胜感激！！！ |
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4楼2008-06-28 20:36:37
2楼2008-06-27 02:06:51
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二楼的高手，以下是我的dock.out文件，请帮忙给分析一下，哪地方出错了？谢谢！ -------------------------------------- DOCK v6.1 Released December 2006 Copyright UCSF -------------------------------------- Molecule Library Input Parameters ------------------------------------------------------------------------------------------ ligand_atom_file lig_charged_aa.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no Orient Ligand Parameters ------------------------------------------------------------------------------------------ orient_ligand yes automated_matching yes receptor_site_file rec.sph max_orientations 500 critical_points no chemical_matching no use_ligand_spheres no Flexible Ligand Parameters ------------------------------------------------------------------------------------------ flexible_ligand yes min_anchor_size 40 pruning_use_clustering yes pruning_max_orients 100 pruning_clustering_cutoff 100 use_internal_energy yes internal_energy_att_exp 6 internal_energy_rep_exp 12 internal_energy_dielectric 4.0 use_clash_overlap no Bump Filter Parameters ------------------------------------------------------------------------------------------ bump_filter yes bump_grid_prefix grid max_bumps_anchor 2 max_bumps_growth 2 Master Score Parameters ------------------------------------------------------------------------------------------ score_molecules yes Contact Score Paramters ------------------------------------------------------------------------------------------ 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 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 500 simplex_final_min no simplex_random_seed 0 Atom Typing Parameters ------------------------------------------------------------------------------------------ atom_model all vdw_defn_file vdw.defn flex_defn_file flex.defn flex_drive_file flex_drive.tbl Molecule Library Output Parameters ------------------------------------------------------------------------------------------ ligand_outfile_prefix output write_orientations no num_scored_conformers_written 1 rank_ligands no ------------------------------------------------------------------------------------------ Initializing Library File Routines... Initializing Orienting Routines... Initializing Conformer Generator Routines... Initializing Bump Filter Routines... Reading the bump grid from grid.bmp Initializing Grid Score Routines... Reading the energy grid from grid.nrg ----------------------------------- Molecule: aa.mol2 Elapsed time for docking: 754 seconds Anchors: 1 Orientations: 500 Conformations: 279 Grid Score: -20.446514 vdw: -20.282318 es: -0.164196 1 Molecules Processed Total elapsed time: 754 seconds |
5楼2008-06-30 16:04:23