On Mon, Feb 20, 2012, Carlos Romero wrote:
> I am using amber11 and i am trying to simulate factor II with ions such
> mercury and magnesium, my question is: do I should change my pdb file
> adding ions manually or, does exist a force field that contain such ions.
> I'm trying to understand what happens to factor II in presence of such ions.
> for your help thanks
Amber has some rather old magnesium parameters, that might be helpful if the
magnesiums are "structural" and always have the same first coordination shell
of ligands. I don't know of any parameters for mercury -- both the metal and
the methyl forms are highly toxic, so be sure to take appropriate precautions.
...good luck...dac
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Received on Thu Feb 23 2012 - 19:00:02 PST
