AMBER Archive (2009)

Subject: Re: [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues

From: case (
Date: Sun Aug 16 2009 - 08:14:14 CDT

On Sun, Aug 16, 2009, Catein Catherine wrote:
> Should I do neutralize the charges in DNA-protein complex with Na+ or
> Mg2+ (before adding solvent) when we generate the prmtop or inpcrd
> files? I found Na+ was used in the tutorial, but some paper used Mg2+,
> why?

This choice almost always has to do with the sorts of experimental conditions
that were used in studies to which the calculations will be compared.


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