On Mon, Jun 13, 2011, Xioling Chuang wrote:
>
> 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?
I don't know. I don't think there are divalent ion parameters included with
the Amber distribution.
> 2. What water model is used for the Amoeba, is it a POL3 model?
No...amoeba uses its own water model; see refs. 15 and 16 in the AmberTools
Users' Manual.
> 3. If I want to use this force field, do I set "ipol=1" in sander input file?
No.
...good luck...dac
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Received on Mon Jun 13 2011 - 05:00:02 PDT
