On Mon, Dec 10, 2012 at 4:09 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Hello All
> I am doing MMPBSA analysis of protein-DNA complex.
> I want to ask a question that why sum of energy of all residue by per
> residue
> energy decomposition is not equal to enthalpy of complex though both have
> same
> energy component?
> In my case sum of energy of all residue is -119.6 kcal/mol and enthalpy of
> complex is 130.4 kcal/mol.
>
> When I checked for MMPBSA tutorial there also two value are not equal
>
No, they should not be equal. By adding up all per-residue contributions,
you are significantly double-counting the non-bonded interactions.
Consider two atoms in different residues. Their interaction should be
counted toward the decomposed, per-residue energy of both residues, but it
should only be included once in the total energy.
Since residues have internal non-bonded interactions, extracting the exact
total energy from the decomposition results is non-trivial.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Dec 10 2012 - 08:00:02 PST
