Re: [AMBER] binding free energy and pose analysis

From: Nitin Sharma <>
Date: Sun, 29 Dec 2013 23:44:24 +0800

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 ?

Sorry for such lame questions

Thanks in advance.

Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : ;

-----Original Message-----
From: case []
Sent: Saturday, December 28, 2013 9:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] binding free energy and pose analysis

On Sat, Dec 28, 2013, Nitin Sharma wrote:
> Can you tell me if it will correct approach to combine MD and
> simulated annealing trajectories?

For most purposes, "no". Simulated annealing trajectories explore a variety of temperatures, in an effort to find an optimal structure. They are not appropriate for use in (say) binding free energy calculations, which are based on an approach that makes use of Boltzmann sampling at a *single* temperature.


AMBER mailing list

AMBER mailing list
Received on Sun Dec 29 2013 - 08:00:02 PST
Custom Search