[Dock-fans] docking resukt problem!!!

Terry Lang terry at cgl.ucsf.edu
Thu Aug 11 10:02:55 PDT 2005


Dear Dock-fan,

>From looking at your input file, I would say one of your problems may be
that you have max_orientations set to 10,000. The default parameters
have been tuned pretty carefully over a wide range of systems. You can
make changes to the parameters and see improvement for your particular
system, but I would not recommend modifying any of the parameters by
more than an order of magnitude. If you want to increase the amount of
sampling in addition to the max_orientations, you can decrease the
min_anchor_size, increase the num_anchor_poses, increase the
number_of_confs_per_cycle, or modify the minimization parameters.

Good luck and let me know if you are still having problems,
Terry

천광우 wrote:

> hello. I,m biochemist.
>
> my first docking result has aproblem. docked regand conformation is
> unstablehindrance.(bumping and large steric hindrance)
>
> tell me, my mistake.
>
> my dock.in file is below.
>
> ---------------------------------------------------
>
> ligand_atom_file lig-124.mol2
> ligand_outfile_prefix lig
>
> limit_max_ligands no
> write_orientations no
> write_conformations no
> initial_skip ! ; 0
> calculate_rmsd yes
> use_rmsd_reference_mol no
> rank_ligands &! nbsp; no
> num_scored_poses_written 1
> orient_ligand yes
> automated_matching yes
> receptor_site_file ! selected_spheres.sph
> max_orientations 10000
> critical_points no
> chemical_matching ! no
> use_ligand_spheres no
> flexible_ligand yes
> ag_conf_search yes
> min_anchor_size &nb! sp; 10
> num_anchor_poses 50
> number_confs_per_cycle 50
> use_internal_energy &n! bsp; yes
> internal_energy_att_exp 6
> internal_energy_rep_exp 12
> internal_energy_dielectric 4.0
> use_clash_overlap &nb! sp; no
> bump_filter yes
> bump_grid_prefix grid
> max_bumps 0
> sc! ore_molecules yes
> energy_score_primary yes
> energy_score_secondary yes
> vdw_scale &! nbsp; 1
> es_scale 1
> nrg_grid_prefix grid
> minimize_ligand &! nbsp; yes
> minimize_anchor yes
> minimize_flexible_growth yes
> minimize_final_pose yes
> use_advanced_simplex_parameters ! ; no
> simplex_max_cycles 1
> simplex_score_converge 0.1
> simplex_cycle_converge 1.0
> simplex_trans_step &nb! sp; 1.0
> simplex_rot_step 0.1
> simplex_tors_step 10.0
> simplex_anchor_min_max_iterations 50
> simplex_flex_min_max_ite! rations 10
> simplex_final_min_max_iterations 100
> simplex_random_seed 0
> atom_model all
> vdw_! defn_file /usr/local/dock.5.2_linux/parameters/vdw_AMBER_parm96.defn
> flex_defn_file /usr/local/dock.5.2_linux/parameters/flex.defn
> flex_drive_file /usr/loc! al/dock.5.2_linux/parameters/flex_drive.tbl
> chem_defn_file /usr/local/dock.5.2_linux/parameters/chem.defn
> max_ranked_ligands 10
> scored_mol_output_override no
> contact_cutoff_distance &nbs! p; 0
> ---------------------------------------------------
>
>------------------------------------------------------------------------
>
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>  
>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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