On Fri, Jul 23, 2010, Xioling Chuang wrote:
>
> I have used amber9 to generate the topology files of poly(AT)
> neutralized with Na+ and K+ ions. As I have looked in the topologies, I
> found that at the flag "%FLAG RADII" the radii of both Na+ and K+ are
> 1.5. My questions are
These are "dielectric radii", that would be used in continuum electrostatic
calculations (like generalized Born or Poisson-Boltzmann). Neither of these
models have been parameterized for explicit ions; rather, mobile ions in
solution are typically treated using Debye-Huckel theory.
So, the radii assigned are simply dummy values, and are not used in any
calculations. (If you were to do implicit solvent calculations, you would
strip out the Na+ and K+ ions before proceeding).
[A note: there *are* folks who are looking at using explicit ions in continuum
solvent simulations. But they are generating their own parameters, and
probably hand-editing prmtop files to implement them. This is an interesting
area for research, but is not (yet?) supported by the way Amber does things by
default.]
...hope this helps...dac
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Received on Fri Jul 23 2010 - 05:00:04 PDT
