On Thu, Dec 13, 2012, Jagur Lambix wrote:
>
> I am trying to set up a simulation for a protein + ligand system with
> polarizable force field (AMOEBA).
>
> My question is that how to set up the parameters for the ligand (an organic
> molecule) in a polarizable condition.
> Can I get any TUTORIAL on it describing the use of AMOEBA in AMBER ?
Tools for setting up an amoeba simulation in Amber are in a somewhat primitive
state. The basic approach is to build your system in Tinker, then convert
to Amber format. The best page I know of is from Pengyu Ren:
http://water.bme.utexas.edu/wiki/index.php/Main_Page
You can find this and other information by typing "amoeba force field in
Amber" into a Google search.
...dac
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Received on Thu Dec 13 2012 - 19:00:02 PST
