Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations

From: David A. Case <>
Date: Thu, 30 Oct 2008 09:17:12 -0400

On Thu, Oct 30, 2008, wrote:

> I have gone through the paper which you mentioned where a similar event. I
> am using the single trajectory approach and i re-checked my input and output
> files. If i want to report the free energy of binding for my system which
> one should i report? What is meant by 'situation of subtracting large
> numbers in an unstable way'?

Since small (percentage) changes in the estimates of solvation energy (e.g. GB
vs PB) make a big difference in the final estimate of binding free energy, you
seem to have a situation where none of the estimates is likely to be very


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Received on Fri Oct 31 2008 - 05:10:37 PDT
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