AMBER Archive (2009)

Subject: [AMBER] Energy-from-MM/PBSA-VS-experiment

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Sun Oct 11 2009 - 07:53:00 CDT

Dear Amber users,

After installing amber10 in my computer yesterday, today I have tried to use MM/PBSA to calculate the binding Energy for my complex. When I obtained the result I found it was -80 Kal/mol, that is really much larger than the experiment value. Based on the formula: Delta-G=-RTlnKd, I can obtained the experimental value is about -11Kal/mol (about 1-10 nM for KD). There is so much difference!

I know here the dis-favorable entropy was neglected, but can entropy really introduce such big diffrence? What really makes me happy is that the total electrostaric energy is really similar with the value calculated using apbs, but using MM/pbsa can really improve the calculation efficiencey!

I have made some revision based on my experience to use APBS, I do not know weather my revision is reasonbale or not. So I have attached it to this email, and hope people here can give me some suggestion.

What is more, I also came across some bugs:
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
But these bugs above, may not influence me to calculate the energy.

Here can anyone give me some suggestion?

Thanks for your help!

Regards,

Rilei Yu ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/



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