AMBER Archive (2007)

Subject: Re: AMBER: Essential ions and water molecules in MMPBSA computations

From: David A. Case (case_at_scripps.edu)
Date: Mon Mar 19 2007 - 09:02:41 CST

On Mon, Mar 19, 2007, Cenk Andac wrote:

> However, the MM-PBSA computations seem to fail with the magnitudes of
> enthalpy and entropy terms of the binding process.

The MM-PBSA method has no way to predict enthalpies and entropies of binding,
only free energies. The continuum electrostatic term is a free energy, and is
not broken into enthalpy and entropy contributions. The "entropy" term in
MM-PBSA is just the configurational entropy of the solute. Since it doesn't
contain the solvent terms, it generally cannot be compared to an experimental
value.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu