AMBER Archive (2009)

Subject: Re: [AMBER] Solvation potential and free energies

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Feb 06 2009 - 07:34:25 CST

On Thu, Feb 05, 2009, guardiani_at_fi.infn.it wrote:

>
> In the Amber9 manual I read that, in order to
> attain the GB/surface-area force field, it is
> sufficient to add to the vacuum force field
> the term (Eq 5.3 of Amber9 Manual):
>
> \sum_{ij}\frac{q_{i}q_{j}}{f^{gb}(R_{ij})} + \sigma*A
>
> This expression, however, is different from the
> one that can be derived from Equations 2 and 3 of
> your paper J. Phys. Chem. B, Vol 104, No 15, 2000.
>
> As I understand, Equation 2 represents the Coulomb
> contribution in a protein-like environment, and this
> term corresponds to the Coulomb contribution in the
> Amber vacuum force-field. In order to account for
> the solvation effects, it is then necessary to add
> Equation 3:
>
> -\frac{1}{2}(\frac{1}{\epsilon_{p}} - \frac{1}{\epsilon_{w}})
> \sum_{ij}\frac{q_{i}q_{j}}{f^{gb}(R_{ij})}
>
> This expression, however, is not the same as
> equation Eq 5.3 of Amber9 Manual due to the
> presence of the factor
> -\frac{1}{2}(\frac{1}{\epsilon_{p}} - \frac{1}{\epsilon_{w}})
>

Eq. 5.3 in the Amber 9 manual is missing the epsilon part of the
equation. This is a misprint.

...dac

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