Re: AMBER: Free energy for part of the system

From: David A. Case <>
Date: Mon, 3 Dec 2007 18:35:50 -0800

On Mon, Dec 03, 2007, jialei wrote:
> We are simulating an 11mer DNA duplex with AMBER9 and willing to compute the
> free energy of the DNA central 5mer by MM-PBSA. I am aware that the MM-PBSA
> has a ligand and receptor selection function to compute the binding energy.
> However, the DNA central 5mer is covalently linked to the rest of DNA. So
> the MM-PBSA does not simply work for this problem. Is there an easy way to
> computer the part DNA's free energy? Thank you very much for the help!

The only relevant quantities that can be computed are free energy
*differences*, and it is not clear what the two end points you are considering

You will need to think carefully about how you want to define the free energy
of part of a molecule, and what you would do with such a number once you
estimated it. It might be possible to make a useful definition (under some
assumptions), but I am pretty sure that there is no "easy way" to do this.

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Received on Wed Dec 05 2007 - 06:07:23 PST
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