AMBER Archive (2004)

Subject: Re: AMBER: AddIons

From: Bill Ross (
Date: Thu Oct 07 2004 - 14:36:24 CDT

> Although I've used AddIons for my peptide in water, I am not
> sure about the use of ions in the case of MeOH and DMSO.

Programmatically speaking (leap):
With water you can solvate then addions and the waters will
be replaced with ions - this may not work with other solvents.

> We don't know if there exist previous experience in this sense, and if
> the ions parameters can also be used in solvents different from water.

The ion parameters were derived for interactions with TIP-style waters,
i.e. large O vdw enclosing the H's. So there is a dependency on a given
simplified polar solvent model, and we found that these vdw parameters
resulted in incorrect distances when the ions were in contact with
atoms from two amber ff's. Therefore we re-parameterized the ions
for ion/amber interactions, deriving equations for choosing the R*
parameter given a cation-oxygen radial distribution peak. See

        Ion-Induced Stabilization of the G-DNA Quadruplex: Free
        Energy Perturbation Studies. W.S. Ross and C.C. Hardin
        Journal of the American Chemical Society 116, 6070 (1994).

Bill Ross
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