AMBER Archive (2009)

Subject: Re: [AMBER] Creating new counterions

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Sep 01 2009 - 14:58:55 CDT

> 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

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