[Dock-fans] Only rescore, energy C6, C12

William Joseph Allen william.joseph.allen at gmail.com
Thu Feb 28 08:03:11 PST 2013


Hi Vaclav,

In order to compute the score of the ligand alone, you will have to choose
"no" for both "orient_ligand" and "flexible_ligand", and "yes" for
"score_molecules". If you choose to use the "continuous_score_primary"
scoring function, then the only input needed are mol2 files of the ligand
and receptor (both with hydrogens and charges added). An example of the
input file needed for that calculation, compatible with DOCK 6.6, is below.
If you want to do a more advanced calculation, consider setting both
"flexible_ligand" and "minimize_ligand" to "yes". This will likely yield a
lower overall energy.

I'm not sure what you mean by your second question. Are C6 and C12
individual atoms in the ligand?

ligand_atom_file                                             <ligand
file.mol2>
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                no
use_internal_energy                                          no
flexible_ligand                                              no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
multigrid_score_primary                                      no
multigrid_score_secondary                                    no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     yes
continuous_score_secondary                                   no
cont_score_rec_filename                                      <receptor
file.mol2>
cont_score_att_exp                                           6
cont_score_rep_exp                                           12
cont_score_rep_rad_scale                                     1
cont_score_use_dist_dep_dielectric                           yes
cont_score_dielectric                                        4.0
cont_score_vdw_scale                                         1
cont_score_es_scale                                          1
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_descriptor_score_secondary                              no
amber_score_secondary                                        no
minimize_ligand                                              no
atom_model                                                   all
vdw_defn_file
~/vdw_AMBER_parm99.defn
flex_defn_file                                               ~/flex.defn
flex_drive_file
~/flex_drive.tbl
ligand_outfile_prefix                                        output
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

Be sure to change the contents of this input file to match your file names
and locations. Then execute dock by:

    $ dock6 -i dock.in -o dock.out

Joe Allen



On Thu, Feb 28, 2013 at 2:53 AM, Václav Bazgier <vaclav.bazgier at upol.cz>wrote:

> Hi,
>
> I would like only rescore natural ligand in some system. Is there any
> way how to do it?
> When I used autodock vina is there command score_only. I have a problem
> with propreties in DOCK 6.6, I dont't know what is correct settings,
> maybe number of orientations or something else?
>
> And my second question?
> Is there any way how to read from result energy C6 and C12?
>
> Thank you for answer and for great program for docking
>
> Vasek
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://mailman.docking.org/mailman/listinfo/dock-fans
>



-- 
William Joseph Allen, Ph.D.
Postdoctoral Associate
Dept. of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/
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