AMBER Archive (2007)

Subject: Re: AMBER: implementation of GB model in AMBER

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sun Jun 17 2007 - 07:58:11 CDT

I think that your confusion is not about GB or PB, but about RESP.
In the Amber force fields, atoms indeed have point charges (and extra
points for some of the force fields, these can be like lone pairs).
You might want to read a bit more on RESP and how it works. In the end
you have point charges and not a grid.

On 6/17/07, john chen <j11chen11_at_gmail.com> wrote:
>
> Dear amber community,
>
> I have a question concerning the implementation of the GB model in AMBER.
>
> I've read the papers by Hawkins, Cramer and Truhlar and those more
> recently by Onufriev, Bashford and
> Case. In these papers, the elecrostatic contribution to the free energy of
> solvation (within the GB model) is
> always described as a sum over pairs of atoms, represented as spheres,
> each with an effective Born radius
> which describes to what extent the atom is buried in the molecule, and an
> effective point charge (located at
> the centre of the sphere). However, in the AMBER force-field, the charge
> density is represented using the
> RESP method, which involves creating a grid of point charges which more
> accurately represent the charge
> density disrtibution of the molecule (or molecular fragment). Does this
> mean that when implementing the GB
> model, the RESP charges are disgarded and Mulliken-like point charges
> centred at each atomic position are
> used instead? In other words, is it correct to say that the RESP charges
> are only used for calculating the
> coulombic interaction term in the force-filed and play no role in the GB
> model for calculating the solvation free energy?
>
> Is this the same for the Possion-Boltzmann method? When the electrostatic
> potential is calculated using the PB equation
> for each charged atom (or each charge site), are the 'charge sites' the
> grid of point charges formulated in the RESP method,
> or has this been replaced by a more simple set of atomic 'single point
> charges'?
>
> with best regards,
> jc.
>
>

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