Re: AMBER: calcium parameter for GB

From: Ji-Lai Li <>
Date: Wed, 17 Jan 2007 00:19:09 -0800

I also encountered this in my simulation although it is in explicit water.
I followed the instruction given by Ross ( when I prepared the and CAL.lib files. Today I checked the RADII and SCREEN of the
prmtop file created with Ca^2+ and two spc waters, just as Chen mentioned,
it looks like below:
C0 O H1 H2 O H1 H2
  1.50000000E+00 1.50000000E+00 8.00000000E-01 1.20000000E+00
  8.00000000E-01 1.20000000E+00
  8.00000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01
  8.50000000E-01 8.50000000E-01

Now I am puzzled about this question. What is the really meaning of the
"RADII" and "SCREEN"? Can you give me some message? Is the RADII and SCREEN
parameter ok for a dynamics simulation?
In addition, the Ca^2+ always escapes from the EF-Hand of the protein in
implicit solvation either minimization or dynamics. However, when explicit
water added, the Ca^2+ is stable in its experimental position during
minimization and dynamics.
Many thanks ~

On 1/16/07, David A. Case <> wrote:
> On Tue, Jan 16, 2007, Wei Chen wrote:
> >
> > I try to simulate a metal protein having calcium ions with GB models.
> The
> > name of calcium ion is defined as 'C0', which is in parm99.dat. When I
> > checked the parmtop file, I found that 'RADII' and 'SCREEN' parameters
> of
> > calcium ions are treated as the same as carbon atoms. So leap somehow
> > recognized 'C0' as carbon atoms. I looked into the unitio.c file. But no
> > parameters of calcium ions are in there. I am wondering if I can find
> > 'RADII' and 'SCREEN' parameters of calcium ions somewhere.
> As far as I know, no one has calibrated GB radii for calcium ions, at
> least in
> the context of Amber potentials. There is a (somewhat old) paper that
> discusses the problem and prospects for this for magnesium, and the same
> principles presumably apply to calcium:
> %A V. Tsui
> %A D.A. Case
> %T Calculations of the Absolute Free Energies of Binding between RNA and
> Metal
> %Ions Using Molecular Dynamics Simulations and Continuum Electrostatics
> %J J. Phys. Chem. B
> %V 105
> %P 11314-11325
> %D 2001
> Maybe others on the list can come up with more recent applications that
> give
> guidance: this is (for sure) at pretty hard problem!
> ...dac
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Ji-Lai Li
State Key Laboratory of Theoretical and Computational Chemistry
Institute of Theoretical Chemistry, Jilin University
People's Republic of China
Tel: 0431-8944710
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Received on Sun Jan 21 2007 - 06:07:03 PST
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