AMBER Archive (2006)

Subject: AMBER: using MM_PBSA just for binding site, feasible ???

From: tonglei (xbcdnana_at_gmail.com)
Date: Sun Mar 12 2006 - 00:53:44 CST

hi:
    I am trying to calculate the binding free energy between a peptide and
protein involved a wil type and a mutant complex
  As we know, due to the mutation of residue, the entropy change shouldn't
be ignored.
  however , it is difficult to compute the free energy for protein-peptide
complex considering the entropy change,
   Is it feasible to use MM_PBSA just for the binding site without other
residues far away the active pocket?

  If it does, could you provide some relevant references ?
  thanks a lot

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