Hi, Ji-Lai,
The 'RADII' and 'SCREEN' are used for GB models (see Manual Page 266). So
they are not used for explicit water. In your case, Calcium ions are set to
the default 'RADII' as unrecognized atoms. Your results show the default
values are not correct for GB models.
Wei
On 1/17/07, Ji-Lai Li <jlutcc.gmail.com> wrote:
>
> I also encountered this in my simulation although it is in explicit water.
> I followed the instruction given by Ross (http://amber.ch.ic.ac.uk/archive/200412/0087.html
> ) when I prepared the frcmod.cal 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:
> ############
> %FLAG ATOM_NAME
> %FORMAT(20a4)
> C0 O H1 H2 O H1 H2
> .............
> %FLAG RADII
> %FORMAT(5E16.8)
> 1.50000000E+00 1.50000000E+00 8.00000000E-01 1.20000000E+00
> 1.50000000E+00
> 8.00000000E-01 1.20000000E+00
> %FLAG SCREEN
> %FORMAT(5E16.8)
> 8.00000000E-01 8.50000000E-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 <case.scripps.edu> 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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> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
>
> --
> 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 - 06:07:10 PST
