Dear Dr. Case,
Thank you for your helpful suggestions regarding the use of AMOEBA.
I will follow the same in TINKER and try to convert in AMBER format.
Thanks
Jagur
On Thu, Dec 13, 2012 at 9:35 PM, case <case.biomaps.rutgers.edu> wrote:
> 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 Fri Dec 14 2012 - 09:00:03 PST
