AMBER Archive (2006)

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

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Fri Apr 14 2006 - 11:49:58 CDT

Hi Vlad,

as this are empirical force fields, the only way to
establish the accuracy limits is to have very many and long tests.
And couple of really high quality reference structures.
We do have (BJ 2004 Reblova et al) protein - RNA complex
(L25 vs 5S rRNA Loop E - Helix IV, ca 25 ns scale, 99 version).
It looks more or less OK, although not all individual H-bonds
were as in the x-ray. On the other side, it is a pretty rigid
system so it easily could be locked around the start geometry.
On the other side, some H-bonds were replaced say by water bridges,
which, frankly, is so tiny balance that it does not necessarily
mean a disagreement.

If anyone else has experience with RNA-protein, I would be happy
to know.

All the best Jiri

> 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..
>
> cheers
> vlad
>
>
>
> 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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> >
> >
>
> --
> 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
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
>
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