AMBER Archive (2009)

Subject: Re: [AMBER] Choice of force feild

From: Gustavo Seabra (
Date: Tue Jun 02 2009 - 09:58:11 CDT

FF03 is a good force field, BUT it used a different design strategy
than gaff and the two are not necessarily compatible. You should use
ff99SB instead. Don't let the naming fool you: ff99SB is actually from
2006. See:

Hornak, V., R. Abel, et al. (2006). "Comparison of multiple Amber
force fields and development of improved protein backbone parameters."
Proteins: Structure, Function, and Bioinformatics 65(3): 712-725.

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
Q: Why do mountain climbers rope themselves together?
A: To prevent the sensible ones from going home.

On Sun, May 31, 2009 at 1:12 PM, manoj singh <> wrote:
> Dear Amber Users,
>  I am relatively new to Amber and have some doubt.
>  I am trying to do FEP calculations to study the effect of mutation on
> binding affinity of the ligand. I have parameterized the ligand using
> antechamber with GAFF. Which version of amber force filed would be best
> choice for me. I am more inclined towards ff03 but I am not sure and
> therefore looking for some expert advise.
> Thanks!
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