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.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,
>
>
>
>
>
> Cricket on your mind? Visit the ultimate cricket website. Enter http://cricket.yahoo.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 06 2009 - 10:05:31 PDT
