[Dock-fans] Need some help about amber score

Carlos P Sosa cpsosa at msi.umn.edu
Fri Apr 4 20:51:28 PDT 2008


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
>
>
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