Re: [AMBER] small molecules

From: David A Case <>
Date: Mon, 10 Nov 2014 17:11:34 -0500

On Mon, Nov 10, 2014, Lara rajam wrote:
> I was interested in simulating the small molecule with
> GAFF force field . I would like to know is there any reference or
> tutorial for calculating the hydration free energies of small molecules
> using amber

See Tutorial A9 at the Amber web site. Some good literature references that
report results like this:

%A D.L. Mobley
%A E. Dumont
%A J.D. Chodera
%A K.A. Dill
%T Comparison of Charge Models for Fixed-Charge Force Fields: Small Molecule
Hydration Free Energies in Explicit Solvent
%J J. Phys. Chem. B
%V 115
%P 1329-1332
%D 2011

%A T. Steinbrecher
%A D.L. Mobley
%A D.A. Case
%T Non-linear scaling schemes for Lennard-Jones interactions in free energy
%J J. Chem. Phys.
%V 127
%P 214108
%D 2007

...good luck.....dac

AMBER mailing list
Received on Mon Nov 10 2014 - 14:30:03 PST
Custom Search