AMBER Archive (2006)

Subject: AMBER: Force field for DNA

From: Osmar Norberto de Souza (osmarns_at_inf.pucrs.br)
Date: Mon Apr 17 2006 - 05:50:31 CDT

Hi Tom,

        I hope all is well.

        It's been quite a while since we last exchange e-mails. I am fortunately returning to DNA
simulations after quite some time and following these discussions in the AMBER list, and even after
your comments below, I still have some doubts. After all, what ff should I use? I will buy AMBER9
and will be simulating DNA and DNA-protein complexes. Any further comments are much appreciated.

        Best wishes,

        Osmar

Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas - LABIO
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Osmar NORBERTO DE SOUZA, PhD |
LABIO | Tel: +55-51-3320-3611 r.24
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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
> similar.
>
> 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
> twist.
>
> 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.
>
> --tom
>
> \-/ 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
> -/-
> /-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
> \-/ BPRP295A http://www.chpc.utah.edu/~cheatham
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