how to calculate the interaction energy between ligand and protein
Clicked A Few Times
8:03:22 PM PDT - Thu, Aug 11th 2011
I used QM\MM method to optimize the protein-ligand complex. protein was in the MM region and ligand is in the QM region. After optimization, I want to how to calculate the interaction energy between ligand and protein. (include the electrostatic and van der Waals interaction energies) Is anyone can help me?

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2:56:37 PM PDT - Wed, Aug 17th 2011
Given the standard output 

------------------------------------------------------------------------

 QM/MM Energy

------------------------------------------------------------------------

 quantum energy                      -537.200184022 (-.141042E+07  kjoule/mol)

 quantum energy adjusted             -537.200184022 (-.141042E+07  kjoule/mol)

 quantum energy internal             -537.135248946 (-.141025E+07  kjoule/mol)

 Bq-nuclear energy                      3.733295197 (0.980177E+04  kjoule/mol)

 Bq-electron energy                    -3.798230274 (-.997225E+04  kjoule/mol)

 classical energy                     -16.117550021 (-.423166E+05  kjoule/mol)

 total qmmm energy                   -553.317734044 (-.145274E+07  kjoule/mol)

------------------------------------------------------------------------

the electrostatic interaction energy can be calculated as sum of "Bq-nuclear energy" and "Bq-electron energy", or as a difference between
"quantum energy" and "quantum energy internal". Vdw interaction energy and others ( e.g. bonded, etc) are unfortunately buried in the "classical energy" term. Please note that a single interaction energy number would likely be meaningless.


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