AMBER Archive (2008)

Subject: Re: AMBER: DNA: GB solvent with salt

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Dec 12 2008 - 05:33:14 CST

you do not need to neutralize it- in fact trying to add explicit ions is
very difficult with GB.
the precaution is that the ions are included in an average way, and if there
are specific ion interaction sites (which are known in DNA), then the model
will have potential weaknesses.

On Fri, Dec 12, 2008 at 4:31 AM, Catein Catherine <askamber23_at_hotmail.com>wrote:

> Dear Sir/Madam,
>
> Do you mind to let me know if I want to do DNA calculations with implicit
> solvent and 0.3M NaCl, do I need to neutralize the charge of the DNA with
> explicit salt like Mg2+ first? Are there any precaution should I play
> attention too?
>
> Best regards,
>
> Cat.
>
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