> I want to create a set parameters or a library file that will allow me to a=
> dd Al3+ counterions to a generic DNA oligonucleotide. If at all possible I=
> would like to be able to use these Aluminum ions like the counterions buil=
> t into Amber10 already such as Na+ or Mg2+. Anybody have any suggestions or=
> know how in this area? Thank you for any help you can provide.
I think ions with charge > |1| are considered a bit dubious for mol mech
methods. Having said that, for deriving vdw you may want to look at
Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
Perturbation Studies. W.S. Ross and C.C. Hardin
Journal of the American Chemical Society 116, 6070 (1994).
The vdw parameters would go in a frcmod. For the ion's topology,
there used to be a script in the distribution for generating ions94.lib
or similarly named; this would show one way of setting this up.
Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 02 2009 - 23:07:28 PDT
