On Mon, Sep 2, 2013 at 9:18 AM, Xioling Chuang <xioling_c.hotmail.com>wrote:
> Dear All,
>
> I have used MM/GBSA to calculate the delta G binding of DNA with Amber12
> and AmberTools12. Next, I installed AmberTools13 and re-compiled Amber12.
> After re-calculating the delta G binding using the same input file (igb=2,
> other parameters were default), the obtained result (including NMODE) are
> different
> AmberTools12: -70 kcal/mol
> AmberTools13: -58 kcal/mol
>
> Why did two versions provide different result? Which one is reasonable?
>
We don't have enough information. I'm assuming you used MMPBSA.py. In any
case, the GB code has remained almost identical, but there have been some
small changes to the standard SA calculation using LCPO. (You can use
molsurf in AmberTools 13 for GB/SA, which is a better option, IMO).
It would be instructive to look at exactly which terms change between
AmberTools 13 and AmberTools 12 to properly diagnose the problem. Without
this information I can't help isolate the problem.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 02 2013 - 09:30:03 PDT
