[Dock-fans] Help: a question about gbsa_hawkins_score_primary
Suhaib Shekfeh
s.shekfeh at gmail.com
Wed Mar 18 01:33:09 PDT 2009
On Wed, Mar 18, 2009 at 9:32 AM, Suhaib Shekfeh <s.shekfeh at gmail.com> wrote:
> because you have specified the Grid score as primary scoring
>
>
>
> On Wed, Mar 18, 2009 at 5:29 AM, thirsty <thirstymail at gmail.com> wrote:
>
>> I have written "gbsa_hawkins_score_primary yes" in dock.in
>>
>> when i run dock6, "gbsa_hawkins_score_primary yes" was deleted, Why?
>>
>> Thank you!!
>>
>> GuanXin
>> 2009.03.18
>>
>> "ligand_atom_file
>> inno-406_ligand.mol2
>> limit_max_ligands no
>> skip_molecule no
>> read_mol_solvation no
>> calculate_rmsd yes
>> use_rmsd_reference_mol no
>> orient_ligand yes
>> automated_matching yes
>> receptor_site_file
>> selected_spheres.sph
>> max_orientations 500
>> critical_points no
>> chemical_matching no
>> use_ligand_spheres no
>> flexible_ligand yes
>> min_anchor_size 8
>> 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 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 grid
>> dock3.5_score_secondary no
>> continuous_score_secondary no
>> gbsa_zou_score_secondary no
>> gbsa_hawkins_score_secondary yes
>> gbsa_hawkins_score_rec_filename inno406.mol2
>> gbsa_hawkins_score_solvent_dielectric 78.5
>> gbsa_hawkins_use_salt_screen no
>> gbsa_hawkins_score_gb_offset 0.09
>> gbsa_hawkins_score_cont_vdw_and_es yes
>> gbsa_hawkins_score_vdw_att_exp 6
>> gbsa_hawkins_score_vdw_rep_exp 12
>> grid_score_rep_rad_scale 1
>> minimize_ligand yes
>> minimize_anchor yes
>> minimize_flexible_growth yes
>> use_advanced_simplex_parameters no
>> simplex_max_cycles 2
>> 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_secondary_minimize_pose yes
>> use_advanced_secondary_simplex_parameters no
>> simplex_secondary_max_iterations 100
>> simplex_secondary_min_add_internal no
>> simplex_random_seed 1
>> atom_model all
>> vdw_defn_file vdw.defn
>> flex_defn_file flex.defn
>> flex_drive_file
>> flex_drive.tbl
>> ligand_outfile_prefix GBSA
>> write_orientations no
>> num_primary_scored_conformers_rescored 1
>> num_secondary_scored_conformers_written 1
>> rank_primary_ligands no
>> rank_secondary_ligands no
>>
>>
>>
>> _______________________________________________
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>>
>>
>
>
> --
> Pharmacist. Suhaib Shekfeh
> Medicinal Chemistry
> Institute of Pharmacy
> Martin-Luther-Universität Halle-Wittenberg
> Wolfgang-Langenbeck-Str. 4
> 06120 Halle (Saale), Germany
>
> Tel: 0049 345 55 25 043
> Fax: 0049 345 55 27 355
> Local Time : GMT + 1
> http://pc.pharmazie.uni-halle.de/akmedchem/mitarbeiter/shekfeh/
>
--
Pharmacist. Suhaib Shekfeh
Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universität Halle-Wittenberg
Wolfgang-Langenbeck-Str. 4
06120 Halle (Saale), Germany
Tel: 0049 345 55 25 043
Fax: 0049 345 55 27 355
Local Time : GMT + 1
http://pc.pharmazie.uni-halle.de/akmedchem/mitarbeiter/shekfeh/
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