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
I have prepared frcmod and off files, available at:
You can use the leaprc.md6 in that archive with leap to load the parameters.
Hope that helps,
On Sun, Aug 16, 2009 at 12:21 AM, Catein
> 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,
> Drag n’ drop—Get easy photo sharing with Windows Live™ Photos.
> AMBER mailing list
AMBER mailing list