AMBER Archive (2009)

Subject: Re: [AMBER] What is the parameters for Mg2+?

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Sun Aug 16 2009 - 11:00:35 CDT

There is a point-charge model of Mg2+ in the AMBER force fields but
this is not a great approximation.

I posted this before, but:

In my simulations I have been using the Mg representation from:

Oeschlaeger et al. Magnesium-cationic dummy atom molecules enhance
representation of DNA polymerase beta in molecular dynamics
simulations: improved accuracy in studies of structural features and
mutational effects. J Mol Biol. 2007 Feb 16;366(2):687-701. Epub 2006
Nov 3.

I have prepared frcmod and off files, available at:

http://atlas.physbio.mssm.edu/~tom/files/MD6.tar.gz

You can use the leaprc.md6 in that archive with leap to load the parameters.

Hope that helps,
--Tom

On Sun, Aug 16, 2009 at 12:21 AM, Catein
Catherine<askamber23_at_hotmail.com> wrote:
>
> Dear Sir/Madam,
>
>
>
> According to the questions and responses posted in the website.  It seems to me that we should not do study Mg2+ effect with AMBER  without calibrations.
>
>
>
> I just wonder if there are starting force field parameters for Mg2+ in AMBER.
>
>
>
> best regards,
>
> Cat
>
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