Re: AMBER: mm-pbsa, long distance free energy calculation problem

From: Bing Liu <>
Date: Thu, 18 Jan 2007 13:09:38 -0800 (PST)

Hi, Wei,
    The energy I calculated is binding free energy, but not including the entropy contribution, that is dG = molecular mechanics energy + solvation free energy

Wei Chen <> wrote:
    I don't know whether you mean binding free energy (dG) or free energy of the complex. Notice that the interaction energy you mentioned should be only mechanical energy, not include solvation energy.
  Wei Chen

  On 1/18/07, Bing Liu <> wrote: Dear Amber user, I use mm-pbsa calculating the free energy of serial protein-protein complexes, in the first try, I didn't calculate the entropy for considering the huge computational power (only include PBTOT).
     In my protein-protein complex, I translate one of the protein around the other in XY planet by every one angstrom, therefore, a serial protein-protein complexes samples were generated. But the result was not as I expected - the longer distance between those two proteins, the weaker interaction energies they will have. The computational result is within a certain distance, the longer distance the weaker interactions (about 14A). But after that, the energy becomes lower (14A to 20A between those two proteins).
     I'm very appreciating to any of your explanations for that?
  Bing Liu

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Received on Sun Jan 21 2007 - 06:07:27 PST
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