AMBER Archive (2009)

Subject: Re: [AMBER] Choice of force field

From: Carlos Simmerling (
Date: Mon Jun 01 2009 - 06:14:09 CDT

you need to tell us more- do you mean best for the ligand, or is it with a
protein, or some other molecule?
for proteins I suggest ff99SB< you can search the archives since there has
been lots of discussion about it in the past.

On Sun, May 31, 2009 at 4:39 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 field 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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