AMBER Archive (2006)

Subject: Re: AMBER: Which one is the best force field for DNA?

From: Thomas E. Cheatham, III (
Date: Fri Apr 14 2006 - 11:01:50 CDT

> Well, I did read sometime ago Tom's review, maybe I missed (or I forgot)
> some of the information there so I'll read it again ...So, I didnt know
> that ff99 (thus also ff03) doses not include the ff98 changes. Is there
> a particular reason why those changes were not included in newer versions?

ff99 does contain a slightly modified set of the ff98 changes; they are
not exactly the same (which likely led to DAC's comments), but very

In ff98, we adjusted angles related to chi and the sugar in an attempt to
improve helical twist (increase it slightly) and to increase chi. This
was successfully accomplished, yet, we appeared to lose some of the
favorable features of ff94 in relation to stabilization of A-DNA in mixed
water/ethanol and with highly charged cations (hexammine cobalt(III)).
So, in some sense, one cannot definitely state that ff98 is "better" than
ff94, just different in that it has a slightly improved overall helical

                     Cornell ff98 ff99
CT-OS-CT-N* V3 1.15 0.383 0.383
             V2 0.0 1.0 0.65

OS-CT-CT-OS V3 0.144 0.144 0.144
             V2 1.0 1.5 1.175

OS-CT-N*-CK V2 0.5 pi 0.0 0.0
 or CM V1 2.5 2.5 2.5

(the "pi" denotes a phase of 180; all other phases are 0 and the numbers
shown are the peak heights).

> If I may, as a short comment on this, I believe that it is important to
> be able to use the same ff for both proteins and nucleic acids (perhaps
> membranes also) as they do coexist and many simulations involve

As a general rule, you do want consistency between force fields such that
if you run proteins and nucleic acids or membranes, there is not a
mis-balance. However, with respect to the ff94->ff99, the only
differences are largely dihedral parameters and not the overall
philosophy. Equivalent methods were used to generate charges, van der
Waals parameters such that all of these variants are compatible. This is
not true when comparing ff94->ff99 with the polarizable ff02 or ff02EP or
the new charge derivation philosophy of ff03 where there could
be-- although this has not been shown to my knowledge-- misbalance.


\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A
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