对接
直接进行半柔性对接，刚性对接不感兴趣 使用指令：
代码语言：javascript复制dock6 -i dock.in
创建文件dock.in 参数详解： http://dock.compbio.ucsf.edu/DOCK_6/tutorials/ligand_sampling_dock/ligand_sampling_dock.html 格式为：
代码语言：javascript复制conformer_search_type flex
write_fragment_libraries no
user_specified_anchor no
limit_max_anchors no
min_anchor_size 40
pruning_use_clustering yes
pruning_max_orients 100
pruning_clustering_cutoff 100
pruning_conformer_score_cutoff 25.0
pruning_conformer_score_scaling_factor 1.0
use_clash_overlap no
write_growth_tree no
use_internal_energy yes
internal_energy_rep_exp 12
internal_energy_cutoff 100.0
ligand_atom_file ../1_struct/lig_charged.mol2
limit_max_ligands no
skip_molecule no
read_mol_solvation no
calculate_rmsd no
use_database_filter no
orient_ligand yes
automated_matching yes
receptor_site_file ../2_site/selected_spheres.sph
max_orientations 500
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 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 ../3_grid/grid
multigrid_score_secondary no
dock3.5_score_secondary no
continuous_score_secondary no
footprint_similarity_score_secondary no
pharmacophore_score_secondary no
descriptor_score_secondary no
gbsa_zou_score_secondary no
gbsa_hawkins_score_secondary no
SASA_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 500
simplex_grow_tors_premin_iterations 0
simplex_random_seed 0
simplex_restraint_min no
atom_model all
vdw_defn_file ../../../parameters/vdw_AMBER_parm99.defn
flex_defn_file ../../../parameters/flex.defn
flex_drive_file ../../../parameters/flex_drive.tbl
ligand_outfile_prefix anchor_and_grow
write_orientations no
num_scored_conformers 20
rank_ligands yes
输入指令,进行运算： dock6 -i dock.in -o dock.out 输出文件： dock.out为总结的参数文件 anchor_and_grow_ranked.mol2为输出文件，里面有20个排名较高的mol 使用chimera查看 Tools->Surface/Binding Analysis->ViewDock 结果，也可以作为动画展示
