Re: [AMBER] regarding forcefield for rna

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 10 Jun 2010 10:14:43 -0700

> 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).


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Received on Thu Jun 10 2010 - 10:30:05 PDT
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