Hi, David and Dear Amber-ers
Thank you so much.
Since TI is not implemented for the amoeba force field. I am wondering if I
can calculate the free energy change
via other method with Amber, such as free energy perturbation or beneett
accptance ratio (BAR)? If yes, I wonder
if I can find any tutorials for that? It seems ren's lab is calculating free
energy via BAR with Amber ("Multipole Electrostatics
in Hydration Free Energy Calculations"), but I am not sure if their amber
has been specifically modified for this purpose.
Any suggestion or comment is very welcome.
Thank you.
yours
libo, NY, USA
2011/8/6 case <case.biomaps.rutgers.edu>
> On Fri, Aug 05, 2011, li he wrote:
>
> > I am trying to calculate the solvation energy of Na+ in water with
> > thermodynamics integration implemented in amber11, sander.
>
> > I copied parameters from ponder's webpage to
> > amber11/dat/leap/parm/amoebapro.prm, created a Na+ offlib file by taking
> > data from
> > amber11/dat/leap/lib/ions08.lib and change the atom type from "Na+" to
> 205,
> > as the original amoeba forefield in amber11 does not
> > have Na+'s parameters.
> > when I calculated the energy cost to turn on the charge of amoeba Na+, I
> > found the DV/DL is alyways 0.
>
> I think you are correct here: TI is not implemented for the amoeba force
> field. Certainly none of the softcore stuff will work. Some interested
> person (Pengyu?) is needed to keep the amoeba implementation going forward.
>
> ....dac
>
>
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Received on Wed Aug 10 2011 - 14:00:02 PDT
