AMBER Archive (2003)

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

From: Peter VARNAI (Peter.Varnai_at_ibpc.fr)
Date: Wed Dec 10 2003 - 10:06:30 CST

Dear Vlad,

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.

Peter

I compared the these parameters in DNA simulations and it is hard to see
> Dear Vlad,
>
> Mg2+ parameters are to be found in the parm91 and parm99 AMBER force-fields
> parm91: 1.10 0.10
> parm99: 0.7926 0.8947
> We use the first set of parameters which seems to provide correct results
> (although polarization and charge transfer effects are not taken into
> account as mentionned by Jiri), see Chem Biol 2003 10 551
>
> Pascal
>
>
> > Dear ambers,
> > Could somebody indicate me some literature where I can find
> > parameters for Mg2+ used in RNA simulations?
> > Thank you very much
> > vlad
>
>
> ________________________
> pascal auffinger
> ibmc-cnrs
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> e-mail: p.auffinger_at_ibmc.u-strasbg.fr
> http://www-ibmc.u-strasbg.fr/upr9002/westhof/biblio_pascal.html
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