AMBER Archive (2004)

Subject: AMBER: positive binding free energy

From: hj zou (
Date: Fri Mar 05 2004 - 00:53:18 CST

Dear amber usersúČ
  I'm performing mm-pbsa and nmode calcultion on a docked protein-ligand complex.
  The mm-pbsa result:PBTOT=-13.50,The nmode result:TSTOT=-23.45.So the binding free energy is a positive value.That's impossible.The ligand binds to the protein with a Kd of 47.3nM(experimental measurements). Why?
  Can anyone give me some suggestions?
  (By the way,I also calculated the binding free energy of another complex which has crystal structure in which another liand bound to the same protein. The calculated results were consistent with the experimental data well.)
  Thanks a lot.
best regards

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