[Dock-fans] Help: Where is my GB/SA score?

[Suhaib Shekfeh]

personally I prefer to use antechamber directly.. I donno exactly if you
have Amber software package.

but anyway when you see that electrostatic interaction zero , most probably
u miss charges in either the protein or the ligand

secondly : as scott said , use the computationally expensive scores like
solvation (GBSA or PBSA) scores and amber scores just for rescoring the
filterated docking solutions not during docking ... try to use combination
of bump , contact and most impostant grid score for docking.

Good docking


On Thu, Mar 19, 2009 at 12:43 AM, Scott Brozell <sbrozell at scripps.edu>wrote:

> Hi,
>
> On Wed, 18 Mar 2009, Suhaib Shekfeh wrote:
>
> > even with Grid score , you have problem with electrostatics .. have you
> > assigned charges for the protein using amber FF and ligands using AM1-bcc
> > ??!
> >
> > On Wed, Mar 18, 2009 at 3:31 AM, thirsty <thirstymail at gmail.com> wrote:
> >
> > > I have set the dock.in file as fowllow:
> > >
> > > gbsa_hawkins_score_secondary                                 yes
> > > gbsa_hawkins_score_rec_filename                              abcd.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
> > >
> > > but I have not receive the GBSA score, the fowllow is my dock.out file:
> > >
> > > Initializing Library File Routines...
> > > Initializing Orienting Routines...
> > > Initializing Conformer Generator Routines...
> > > Initializing Grid Score Routines...
> > >  Reading the energy grid from grid.nrg
> > > Initializing Hawkins GB/SA Score Routines...
> > > -----------------------------------
> > > Molecule: inno-406_ligand-ch3.mol2
> > >  Elapsed time for docking: 67311 seconds
> > >  Anchors:  3
> > >  Orientations:  1500
> > >  Conformations:  618
> > >  Primary Score
> > >     Grid Score:          -58.790798
> > >            vdw:          -58.790798
> > >             es:            0.000000
> > >
> > > Why not I get the GBSA Score?
>
> You specified GBSA Score as the secondary score.
> Secondary scoring starts after primary scoring; presumably your
> ligand file contains more than one ligand.
>
> In general, you should start small with a known example and incrementally
> modify that to your actual project.  So start with the tutorials and
> modify the inputs to use GBSA Score, etc.
> Then you won't have to wait for 67311 seconds to see what's what.
> This approach should also help avoid the problems mentioned
> by Suhaib Shekfeh.
>
> Scott
>
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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/
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