Honestly, the difference between -138 kcal/mol and -134 kcal/mol does not
seem that large to me, especially given the difference in the number of
frames (1 vs. 20) and the error of the MM-PBSA method. Naturally, there will
be some variance in binding energy between each frame, but the binding
energy will eventually converge with enough frames. I have found that
usually ~200 frames is sufficient to capture the binding energy using
MM-PBSA. Using less than 200 frames usually does not sample enough
conformations to converge the binding energy, and using more than 200 frames
does not result in the binding affinity changing any more. Once again, this
is my experience and results may vary by system, too.
I hope this helps.
-Bill
On Mon, Aug 30, 2010 at 10:12 AM, shenna shearin <smsheari.gmail.com> wrote:
> Hello:
>
> I am doing a free energy run using MMPBSA on a large system (~116,000
> atoms). I notice that the more frames I use the lower the free energy term
> gets. I tried running MMPBSA on 1 frame and 20 frames and the corresponding
> free energy values were -138 kcal/mol and -134, respectively. Can someone
> tell me what is the most amount of frames I should use to get a reasonable
> free energy value?
> --
> Shenna
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Aug 30 2010 - 09:00:03 PDT
