AMBER Archive (2005)

Subject: Re: AMBER: Mg2+ issues of using MM-PB/GBSA

From: mingche Pan (panmingche_at_yahoo.com)
Date: Fri Dec 02 2005 - 10:32:15 CST


Were these differences observed with the same radii for Mg2+ and everything else, i.e. using the radii in the same prmtop file (for pbsa, this means using the radiopt=0)?

  ---------------------------------------------------------------------------------------------------------------------
  Thanks for the replies from profs. Simmerling, Luo, Case and Cheatham. To be more specific, I have a same ligand bound to the same protein, but in different binding sites. ligand has the direct interactions with the Mg2+ ion in one of the binding site. Here are the results.
   
             
     
    Mode 1 (binds to Mg2+)
    Mode 2 (no interactions with Mg2+)
       
    Mg radius
    0.99
    1.18
    1.45
    0.99
    1.18
    1.45
       
    GB(amber6_1)
    -33.23
    -59.89
    -83.98
    -35.83
    -36.03
    -36.25
      AMBER8
    GB(mbondi_1)
    -38.62
    -65.14
    -89.16
    -40.06
    -40.23
    -40.42
       
    GB(bondi_2)
    -10.06
    -47.89
    -78.80
    -30.07
    -30.28
    -30.52
       
    GB(bondi_5)
    -96.39
    -118.38
    -127.18
    -67.04
    -66.42
    -64.90
       
    GB(mbondi2_2)
    -15.96
    -53.34
    -83.92
    -34.74
    -34.86
    -35.01
       
    GB(mbondi2_5)
    -93.93
    -116.39
    -128.98
    -70.60
    -69.70
    -67.65
       
    PB
    -42.45
    -42.45
    -42.44
    -32.76
    -32.76
    -32.76

   
  The mode 2's results look more reasonable than those of mode 1. I guess it is because the binding mode 2 has less effects from Mg2+. For the mode 1, the exposure of Mg2+ could be very different in the complex and protein system.
   
  I am not sure why there is no difference between PB model when adopting different radii.
   
  Any further suggestion? Thanks in advance!
   
  Mingche
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   

                
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