AMBER Archive (2003)

Subject: Re: AMBER: Mg2+ parameters for RNA usage

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Dec 10 2003 - 12:07:49 CST

> An additional parameter set for Mg2+ that I adapted based on the latest
> numbers from Aqvist:
>
> Mg 0.6245 28.4444 Mg2+ Aqvist THEOCHEM 1992 (adapted)
>
> The numbers look quite different from the ones previously mentioned
> (steeper potential at short distances with a deeper minimum in the
> Mg...Ow potential), but this should give accurate solvation free energy
> for TIP3P water and a correct rdf-peak.
 
Per the Ross and Hardin paper (which I don't recall covering
divalent ions), the Aqvist parameters are not unique in
satisfying solvation free energy and 1st rdf peak. A formula
is presented there for finding R* for a fixed well depth for
monovalent ions. Note that Aqvist parameters need to be adapted
for Amber vdw combining rules, the details of which should be
covered by one of the Amber FAQs.

Also note that, per our paper, ion vdw parameters derived for water
models that have a "fat oxygen" vdw enclosing point-charge-only
hydrogens (such as TIP* and SPC) do not work for ions in contact
with atoms with 'normal' radii i.e. solute atoms.

And as others have pointed out, divalent ions are somewhat
beyond the limitations of the force field, so be sure to factor
this into experiment design and interpretation of the results.

Bill Ross

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