Hello,
This radii means nothing outside the context of an implicit solvent
calculation, so you can consider this to be a dummy variable. The VDW
radius is mixed up in the LENNARD_JONES_A/BCOEF arrays, and you have to
apply the combining rules in reverse to extract the radii from the prmtop
(but it should also be in the parameter files).
This is a dummy variable because simulating explicit ions in implicit
solvent is atypical, as salt effects are included implicitly as well through
a debye-huckel parameter in GB solvents.
Hope this helps,
Jason
On Mon, Aug 30, 2010 at 1:15 PM, zhihong ke <ebelleke.gmail.com> wrote:
> Hello.
>
> In my system, there is a Ca2+ ion.
> I have download its parameter from the
> http://www.pharmacy.manchester.ac.uk/bryce/amber.
> Then, I found the in the prmtop file, the modified Bondi radii for Ca2+ and
> Na+ is 1.500.
> Why they share the same radii?
> And is it right?
>
> Thank you very much!
>
> Zhihong
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 30 2010 - 10:30:06 PDT
