On Fri, May 17, 2013 at 12:00 AM, Sun <sunbintyy.163.com> wrote:
> Dear All,
> I want to model a system containing an aluminum ion ( Al 3+) and so I need
> the force field parameters for the ion . I have searched the default parm
> files in Amber and finding no items about alumimun. I have also searched
> the information about aluminum through some periodictable websits and no
> van der waals radius could be found. So could anyone give some advice about
> how to generate the force fieds parameters of Aluminum Ion ?
>
My guess is that these parameters can't be found because they don't exist.
Divalent metal ions are notoriously difficult to parametrize given their
large charge and the amount of polarization that occurs in the hydration
shell around them. There has been considerably effort put into getting
these ions to behave 'better' in simulation, given the importance of
magnesium and calcium ions in physiological environments. I think the
general consensus is that 2+ ions are at the very edge of what fixed-charge
force fields are able to handle with the standard 12-6 potential.
3+ charges are even worse, and I would not be surprised if there was no set
of acceptable vdW parameters that would 'work' for Aluminum. I would
suggest looking for any literature in which people have done what you're
trying to do and look at their approach. You may need to create a hydrated
residue with the aluminum explicitly bound to its solvent shell, with an
appropriately adjusted charge distribution accounting for the polarization
effects. But I don't have much experience with this so it's all
speculation.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 14 2013 - 09:00:03 PDT
