With the single trajectory protocol, all of the internal energy terms
cancel out because the coordinates for the complex, receptor, and ligand
are exactly the same. So if you sum those terms for the receptor and
ligand, the sum will always be the same as the corresponding terms for the
complex (as long as you have consistent parameters across all prmtop
files). However, the internal terms are calculated and do contribute to
delta G binding if the triple trajectory approach is applied, where a
different trajectory is supplied for the complex, receptor, and ligand.
I hope that helps.
-Bill
On Mon, May 28, 2012 at 2:02 AM, Xioling Chuang <xioling_c.hotmail.com>wrote:
>
> Dear All,
>
> For calculating the G total using mmpbsa.py of AmberTools 1.5, the G total
> is the sumation of G gas and G sol. However, it seems that only VDWAALS and
> EEL terms are tanken into account for G gas, not internal energy terms
> (bond, angle, dihedral, 1-4VDW and 1-4EEL). Is this reasonable for G gas
> calculation? If so, how can the internal terms contribute to G binding?
>
> Best Regards,
> Xioling
>
>
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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 May 28 2012 - 05:00:02 PDT
