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)?
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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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Received on Fri Dec 02 2005 - 16:53:01 PST
