[Dock-fans] grid score calculation

[Suhaib Shekfeh]

be sure to tell the program to perform only scoring , it seems you didnt
> disabled the docking procedure .. use an input file like this:
>
> ligand_atom_file                                             xx.mol2
> limit_max_ligands                                            no
> skip_molecule                                                no
> read_mol_solvation                                           no
> calculate_rmsd                                               no
> orient_ligand                                                no
> flexible_ligand                                              no
> bump_filter                                                  no
> receptor_site_file
> selected_spheres.sph
> max_orientations                                           (  1000 )
> critical_points                                              no
> chemical_matching                                            no
> use_ligand_spheres                                           no
> score_molecules                                              yes
> contact_score_primary                                        no
> contact_score_secondary                                      no
> grid_score_primary                                           yes
> grid_score_secondary                                         yes
> 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                                 no
> amber_score_secondary                                        no
> minimize_ligand                                              yes
> simplex_max_iterations                                       1000
> 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_final_min                                            no
> simplex_random_seed                                          0
> atom_model                                                   all
> vdw_defn_file
> /prog/dock6.2/parameters/vdw_AMBER_parm99.defn
> flex_defn_file
> /prog/dock6.2/parameters/flex.defn
> flex_drive_file
> /prog/dock6.2/parameters/flex_drive.tbl
> ligand_outfile_prefix                                        output
> write_orientations                                           no
> num_scored_conformers                                        1
>
>
>
>
> On Mon, Mar 30, 2009 at 12:35 PM, Prashant Kumar <prashantkbio at gmail.com>wrote:
>
>> Dear all,
>>              I want to calculate the grid score with out performing
>> docking calculation. So for that when made some changes in the anchor.infile like orient_ligand no the program give me some false score that is in
>> positive value. If any body have did this type of calculation before the
>> kindly tell me how's the input file look like. I would like to mention one
>> more thing that when I am reducing the max_orientations below 10 then also i
>> am not geeting the result.
>>
>> --
>> Prashant Kumar
>>
>>
>> _______________________________________________
>> Dock-fans mailing list
>> Dock-fans at docking.org
>> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>>
>>
>
>
> --
> 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/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20090330/06dd7256/attachment.html