> You should include ions,
> one per each cavity.
> Use Na+ instead, K+ are oversized.
This paper has lots on this issue, including reparameterizing
ions for quadruplex vs. water:
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).
Bill
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Received on Thu Jun 10 2010 - 10:30:05 PDT
