AMBER Archive (2006)

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

From: Thomas Cheatham (
Date: Mon Oct 30 2006 - 20:15:18 CST

> 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

I am by no means an expert here, but I beleive that the polarizable force
fields in Amber have not been as extensively tested as their additive
counterparts. Given this, it is not clear to me whether they have the
same biases; but, likely (and again in my opinion), there are biases.
The extensive database of Simmerling's group could be used to test this.
In addition to possible biases, the polarizable force fields were merely
grafted onto the existing force fields (without extensive validation) and
I further worry about inconsistencies in the model, such as the 1-4
exclusion scaling and lack of 1-2 and 1-3 polarization. This is a point
of debate.

> My application is to study a solvated peptide in explicit water and have
> settled on testing ff99SB with TIP3P but would like to try a polarizable
> comparison. Would ff02pol.rl with POL3 provide a reasonable comparison?

If I were to do this, I would recommend comparing ff99sb and maybe ff03
(although we have been getting more consistent behavior in coiled-coil
models with ff99sb) and then jump into the AMEOBA force field in Amber.
I think that Ponder and his group have published protein parameters but
should note that the computational cost is considerable.

Also, in the past people have tried to use polarizable water with additive
protein, i.e. mixing ff99sb w/ pol3; but the real question is: why do you
want to do the comparison? Is it to validate/improve force fields or see
if you see "different" results? In the latter case, how do you know what
is the "correct" behavior (without comparison to experiment). Comparison
to experiment should be the ultimate goal/aim... I am fully supportive of
testing multiple force fields models, but you should have an end-point to
judge their validity.

I am sure others will chime in with their opinions (noting that all of us
have opinions, some have experience, and the best is opinions/experience
validated by experiment)...


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