AMBER Archive (2008)

Subject: AMBER: Bennett acceptance ratio with Amber10

From: Samuel Genheden (a03samge) (a03samge_at_student.his.se)
Date: Tue Aug 26 2008 - 06:58:13 CDT

Hello, Amber users

I would like to know if it is possible to use the Bennett acceptance ratio method with Amber 10 to calculate free energy differences? I'm aware about the theory behind the method but I would like to know how to set up the systems in Amber 10.

I've started a project were I've calculated dG of some ligand-protein systems using TI and by using the scheme in the TI tutorial for Amber 10. Is it possible to use some data or the trajectories from these simulations when calculating the Bennett acceptance ratio? Is it gonna work with the soft-core potentials?

Best regards,
Samuel Genheden
Lund university, Sweden

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