AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 30 2006 - 20:57:48 CST

On Mon, Oct 30, 2006, Thomas Cheatham wrote:
>
> > My question is: has the ff02pol.rl addressed the same backbone dihedral
> > "problems" that ff99SB has addressed, or is the ff02pol.rl still likely to
>
> 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)

It is indeed somewhat hard to directly compare the published ala-3 reults for
ff99SB with the ala-7 for ff02pol.r1. But it seems a little harsh to say that
the latter was "merely grafted onto the existing force fields withoug
extensive validation".

I don't myself have any really good answer to the original question, however.
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
well).

As they say, just my $.02.

...dac
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