Thank you Jason for explanation.
> 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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Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Dec 10 2012 - 11:00:01 PST
