Re: [AMBER] binding free energy and pose analysis

From: Jason Swails <>
Date: Sun, 29 Dec 2013 12:10:31 -0500

On Sun, Dec 29, 2013 at 10:44 AM, Nitin Sharma <>wrote:

> Dear dac,
> Thanks for the reply. My concept got more clear.
> I would like to ask one more thing. As far as I know the binding free
> energy is calculated as an average over all the frames of the trajectory so
> this will be valid for all any pose in the trajectory. However, if I
> select the final pose from simulated annealing will the binding free energy
> calculated from molecular dynamics be valid ?

I don't quite understand what you're asking. Without reweighting simulated
annealing snapshots using something like MBAR, snapshots from simulated
annealing cannot be used to compute binding free energies.

If you are talking about starting molecular dynamics from a final pose
generated from simulated annealing, that would work as long as that
structure is equilibrated previously.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Dec 29 2013 - 09:30:02 PST
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