There are known differences between the default values for regular PB
versus decomposition PB because of the limited options available in the
code for decomposition analysis. If you examine the mdin (or even mdout)
files created MMPBSA.py for running the calculations, you should see
distinct differences between the variables present in each. If you make the
variables consistent (i.e. only use options available to decomposition with
your regular PB calculations) then you should be able to reproduce exactly
the binding energy between regular and decomposition PB analysis.
I hope that helps.
-Bill
On Tue, Jun 19, 2012 at 12:57 AM, marawan hussain
<marawanhussain.yahoo.com>wrote:
> Dear AMBER users,
> I'm trying to calculate the binding energy of a ligand-protein complex
> using the MMPBSA script. The PBSA results are different with/without the
> free energy decomposition although they supposed to be the same..I'm using
> AMBER12...When i examine carefully, i noticed a new term, E dispersion
> introduced when i ran free energy decomposition, is this term is
> intentionally made as default in the MMPBSA uponenergy decomposition...???
>
> Thanks in advance
>
> Marawan
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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 Tue Jun 19 2012 - 19:00:03 PDT
