AMBER Archive (2004)

Subject: AMBER: PMF correction factor

From: Harvey, David Richard (
Date: Tue May 04 2004 - 08:35:13 CDT

I was wondering if AMBER 8 can implement PMF correction calculations for a double
annihilation FEP experiment involving a ligand with two aromatic rings. Previous
attempts with AMBER 7
have resulted in errors due to constrained rings and a different program altogether was
recommended. Annihilating the ligand will undoubtedly cause PMF errors for
this experiment and it would be very helpful to know of any improvements in GIBBS or
SANDER in AMBER 8 which may solve this problem.
Thank you very much.
-David Harvey
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