AMBER Archive (2009)

Subject: Re: [AMBER] where to I get the parameters for Mg divalent ion

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Thu Jun 18 2009 - 22:53:01 CDT

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 Thu, Jun 18, 2009 at 12:11 AM, Mannan<malie_03_at_yahoo.co.in> wrote:
> Hi AMBER peoples,
>
> I would like to do MD for Mg bound protein, so I need parameters fo Mg.
> But I couldn't find it in http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
>
> How do I get the parameters for Mg, anyother paper/site
>
> Kindly Help,
> Mannan,
>
>
>
>
>
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