[AMBER] The differences of MMPBSA calculations between AT1.5 andAT12, especially in PBSA solvation model.

From: <gjtigergj.163.com>
Date: Fri, 30 Nov 2012 11:05:52 +0800

Hi Amber users,

I met a problem about the differences between AT1.5 and AT12.

The complex was a protein-protein model, and the binding energy was calculated through MMPBSA.py.

In spite of the same trajectory and the same input parameters, there was significant difference between AT1.5 and AT12 in PBSA solvation model.

The energies were listed below. In GBSA model, the results are almost the same. However, it differs a lot for G solv values and AT12 always show positive binding energy.

Could someone tell me the reason behind it? The item EPB increased by 10% in AT12, why? And what's the difference between ECAVITY in AT1.5 and ENPOLOR & EDISPER in AT12?

Thanks a lot,

Jianrong Xu

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Received on Thu Nov 29 2012 - 19:30:02 PST
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