AMBER: Regarding free energy calculation and covalent bond

From: nag raj <>
Date: Mon, 20 Aug 2007 21:07:04 -0700 (PDT)

Dear Amber users,
                                       I want to calculate free energy of binding between DNA and ligand. But ligand forms covalent bond with DNA. Here I am giving general equation of my system (DNA and ligand) forming covalent bond complex.
  (DNA)G-NH2 + R-C=N-R1 (ligand) ----->
                                                                  G-NH-CRH-NH-R1 (complex)
  My question is how to calculate free energy of complex?
  Any suggestion is appreciated
                                                                            With best regards,
                                                                             Nagaraja Mulpuri.

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Received on Wed Aug 22 2007 - 06:07:31 PDT
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