[Dock-fans] Need some help about amber score

Äî Áõ yolanda.only at yahoo.com.cn
Mon Apr 7 01:02:35 PDT 2008


Dear all:
   
  First of all, I really appreciate Carlos' reply. Maybe because I didn't interpret my last problems clearly, the reply is not what I expected. 
  The fact is that I have tried the amber tutorial and got the result "dock.out". And I found that the result in the dock.out file is as follows:
   
  Molecule: AAH
   Elapsed time for docking: 71 seconds
   Anchors:  1
 Orientations:  1
 Conformations:  1
     Amber Score:           -5.119654
       complex:        -4658.695412
      receptor:         4584.941716
        ligand:           68.634042
The problem puzzling me is what does the negative (or positive) of complex (or receptor) represent for? I know that negative amber socre represent for good binding .But how about the others? The result of my own complex is as follows:
  ##########  Name:  ZINC00242930
> ##########   Amber Score:          -23.744446
> ##########       complex:              1312969.508014
> ##########      receptor:              -1312992.442160
> ##########        ligand:               -0.810299
Why the energy of my complex is positive? Is that bad?
  Sorry for another question. I noticed that the amber tutorial said :
  EMM = EvdW + Ees + Eint ---- obtained from AMBER MM potentials.
  What is "Eint". I remember that, in grid based score, Eint=Evdw+Ees. How about the equation above? 
  At last, please forgive me for lack of knowledge of molecular mechanics.
  Any answer would be appreciated!
   
   
  Best regards,
   


Yolanda Guo
Northeast Normal University   

       
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