Re: [AMBER] Efficient, accurate estimation of relative binding free energies

From: Jason Swails <>
Date: Mon, 30 Jun 2014 06:17:01 -0700

On Mon, Jun 30, 2014 at 5:13 AM, Guo, Zhuyan <> wrote:

> Hi,
> We are interested in methods in efficient, accurate estimation of relative
> ligand binding free energies that quickly rank/priorities compounds in
> congeneric series such as in a lead optimization paradigm in drug
> discovery. One example of such techniques is the L-dynamics method that can
> evaluate multiple ligands simultaneously from a single MD run. It is
> currently implemented in CHARMM. Here is a reference to most recent work
> from Dr. Brooks' lab at the University of Michigan:
> Knight JL, Brooks CL, III. Multisite λ Dynamics for Simulated
> Structure-Activity Relationship Studies. J. Chem. Theo. Comput.
> 2011;7(9):2728-39
> Has anyone ported L-dynamics to AMBER or know of similar code for the
> AMBER platform?

​No, lambda-dynamics has not been ported to Amber.​

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jun 30 2014 - 06:30:02 PDT
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