Re: [AMBER] binding free energy and pose analysis

From: Nitin Sharma <>
Date: Mon, 30 Dec 2013 01:23:58 +0800

Respected sir,

I have a scenario where I want to differentiate between active and inactive ligands. For that purpose I ran 30ns MD simulation. However, the final poses were not convincing enough. So I thought to do simulated annealing from the pose attained after the MD for 1ns. I got the poses but I also wished to calculate the binding free energy which i will do from the 30ns MD simulations trajectory.

Now I have final pose which resulting from simulated annealing and binding free energy from MD simulation. So I wanted to know will be the binding free energy calculated from MD will be valid on the pose from simulated annealing or only on the poses present in the trajectory used to calculate binding free energy.

Also can you give me something new to read " reweighting simulated annealing snapshots using something like MBAR to calculate binding free energy". I would try to find out more about this but any reference for it would be helpful.

Thanks and regards,
Nitin Sharma

-----Original Message-----
From: Jason Swails []
Sent: Monday, December 30, 2013 1:11 AM
To: AMBER Mailing List
Subject: Re: [AMBER] binding free energy and pose analysis

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 - 09:30:03 PST
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