AMBER Archive (2009)

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

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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.

...dac

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• Previous message: case: "Re: [AMBER] Can I do DNA bending with AMBER?"
• In reply to: Catein Catherine: "[AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues"
• Next in thread: Ross Walker: "RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?"
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