AMBER Archive (2005)

Subject: Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon Jun 06 2005 - 02:23:16 CDT

Dear amber users,

> > Does anyone has a optimized radius parameter for Mg2+ ion in mm_pbsa calculation?

I have found the 0.99A radius in the MM-PBSA parse radii file to be a
little small. There is some papers that discuss a Mg radius of 1.45A:

Hughes S.J.; Tanner J.A.; Hindley A.D.; Miller A.D.; Gould I.R. 2003 BMC Struct. Biol. 3, 5

Minehardt T.J.; Cooke R.; Pate E.; Kollman P.A. Biophys. J. 80, 1151

You could always optimize the radius yourself to obtain correct
experimental solvation free eenrgies

Kind Regards,

Thomas

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