AMBER Archive (2006)

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

From: Vlad Cojocaru (
Date: Fri Apr 14 2006 - 11:30:23 CDT

Hi Tom, Jiri, David, all ambers

Now, what about ff03? According to your opinion, is it recommended to be
used in protein-nucleic acids complex simulations? Or is it "safer" to
stick to ff99 for that purpose? It would be interesting if anybody has
done simulations of protein-RNA or protein-DNA complexes with ff03 and
compared them to simulations done with ff99..


Thomas E. Cheatham, III wrote:

>>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
>The AMBER Mail Reflector
>To post, send mail to
>To unsubscribe, send "unsubscribe amber" to

Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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