A few divalent ions have been parameterized in Amoeba, including mg2+, ca2+,
and zn2+. Unfortunately, as David said, Amber might not have them yet. Check
with Ren lab about the parameters for divalent cations.
On Mon, Jun 13, 2011 at 5:02 AM, Xioling Chuang <xioling_c.hotmail.com>wrote:
>
> Dear All,
> As stated in Amber11' manual (page 83), the Amoeba force field can be used
> for water and univalent ions. So my question are,
> 1. Can this force field be used with divalent ions?
> 2. What water model is used for the Amoeba, is it a POL3 model?
> 3. If I want to use this force field, do I set "ipol=1" in sander input
> file?
>
> Thank you very much in advance.
>
> Regards,
> Xioling
>
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Received on Mon Jun 13 2011 - 09:00:02 PDT
