[Dock-fans] Need some help about amber score

[Carlos P Sosa]

Hello,

The Amber score tutorial defines what the terms are and provides useful
information:

http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm

Hopefully this helps.

> Dear dock-fans:
>
>   I have tried the amber score tutorial and found that the result in the
> output_scored.mol2 file is as follows:
>   ########## Name:  AAH
> ##########   Amber Score:           -4.254279
> ##########       complex:        -4657.768593
> ##########      receptor:         4584.941716
> ##########        ligand:           68.572598
>
>   I know that the negative amber scores represent good binding, but I
> don't understand what does the negative or positive of the complex(
> receptor ,ligand ) mean.
>   I also have tried my own target and obtained the result is as follows:
>
>   ########## Name:  ZINC00242930
> ##########   Amber Score:          -23.744446
> ##########       complex:      1312969.508014
> ##########      receptor:     -1312992.442160
> ##########        ligand:           -0.810299
>
> Obviously, the energy of my complex is positive and the receptor is
> negetive. What do they represent for?
>   And the result of grid based score is as follows:
>
>   ########## Name:  ZINC00242930
> ##########    Grid Score:          -48.303177
> ##########           vdw:          -43.241596
> ##########            es:           -5.061582
>
>   I would appreciate any think and comment!
>
>   Best regards,
>
>
> Yolanda Guo
> Northeast Normal University
>
>
> ---------------------------------
> You rock. That's why Blockbuster's offering you one month of Blockbuster
> Total Access, No Cost._______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>