Thank you Tom.
I will try to use it. : )
Best regards,
Cat
> Date: Sun, 16 Aug 2009 12:00:35 -0400
> Subject: Re: [AMBER] What is the parameters for Mg2+?
> From: ttjoseph.gmail.com
> To: amber.ambermd.org
>
> 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.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
> >
> > _________________________________________________________________
> > Drag n’ drop—Get easy photo sharing with Windows Live™ Photos.
> >
> > http://www.microsoft.com/windows/windowslive/products/photos.aspx_______________________________________________
> > 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
_________________________________________________________________
Share your memories online with anyone you want.
http://www.microsoft.com/middleeast/windows/windowslive/products/photos-share.aspx?tab=1_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 23:15:42 PDT
