Re: AMBER: ff99SB vs ff02 (ff02pol.rl)

From: Thomas Cheatham <>
Date: Mon, 30 Oct 2006 22:07:46 -0700 (Mountain Standard Time)

> > In addition to possible biases, the polarizable force fields were merely
> > grafted onto the existing force fields (without extensive validation)....
> I'll jump in a little here, if only to keep Yuan and Piotr from feeling
> put upon.... :-)
> Certainly, everyone interested in this should study the paper that
> describes ff02pol.r1:
> Z.-X. Wang, W. Zhang, C. Wu, H. Lei, P. Cieplak, and Y. Duan. Strike a
> Balance: Optimization of backbone torsion parameters of AMBER polarizable
> force field for simulations of proteins and peptides. J. Comput. Chem. 27,
> 781-790 (2006)

Yes, I am sorry here that I mis-represented the comparison. I was
thinking about the older ff02 polarization model, not the ff02pol.r1. The
revision one (r1) model is a very useful benchmark and comparison...

> I've run folded protein simulations with pretty similar results for both
> ff99SB and ff02pol.r1. If you are going to go into the peptide field
> (especially for just alanine-based peptides) you better be prepared for a lot
> of controversy--that's partially what makes it kind of fun (but frustating as

As pointed out by David Case, for proteins all of these models seem to do
a reasonable job. I also know that Wang, Cieplak, Duan and co-workers put
significant efforts into balancing the intra- and inter- molecular
hydrogen bonding in these force fields. Given this, acknowledging my
oversight with equivalencing ff02pol with ff02pol.r1 in my mind, I
highly recommend comparing multiple of these force fields including
ff99sb, ff02.r1 and the AMOEBA force fields.

Sorry for the confusion,

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Received on Wed Nov 01 2006 - 06:07:23 PST
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