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

[Suhaib Shekfeh]

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?
>
> Thank you!
> GuanXin
> 2009.03.18
>
>
>
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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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