[Dock-fans] Need some help about amber score

Äî Áõ yolanda.only at yahoo.com.cn
Fri Apr 4 18:37:58 PDT 2008


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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