Very kind of you Kevin.
Some of the articles I do have.
The parameter article as a reference to what I am aiming is
[1] Ponder, J. W., and Case, D. A. Force fields for protein simulations.
Advances in Protein Chemistry 66 (2003), 27–85.
It's an excellent review, the only point it's 2003.
Cheers,
Alan
On Wed, May 12, 2010 at 17:45, Kevin Hauser <84hauser.gmail.com> wrote:
> Hi, Alan,
>
>
>
> I was not able to find what (I think) you wanted, but came across some
> things that may be helpful (?):
>
> Website:
> http://www.bmb.uga.edu/wampler/8200/using-ff/mmrefs.html
> (See bottom of page for "comparisons" - none of which are recent, though)
>
> Loosening your <3 year constraint, the following articles:
>
> Geometry and excitation energy fluctuations of NMA in aqueous solution with
> CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein
> ultraviolet spectra simulation*. Chem. Phys. Let. 2008
> *Zhenyu Li, Haibo Yu, Wei Zhuang and Shaul Mukame
> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2344158/)
> * *
> and
> Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of
> the
> Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS *J.
> Chem. Theor. Comput. 2006*
> U. Deva Priyakumar and Alexander D. MacKerell, Jr
> (http://pubs.acs.org/doi/abs/10.1021/ct0501957)
>
> and
>
> Assessment of standard force field models against high-quality *ab
> initio*potential curves for prototypes of
> -, CH/, and SH/ interactions
> *Journal Comp. Chem. 2009*
> C. David Sherrill, Bobby G. Sumpter, Mutasem O. Sinnokrot, Michael S.
> Marshall, Edward G. Hohenstein, Ross C. Walker, Ian R. Gould
> (http://www3.interscience.wiley.com/journal/122218931/abstract)
>
> and
>
> A consensus view of protein dynamics *PNAS 2006*
> Rueda, M; Ferrera-Costa, C.; Meyer, T; Perez, A; Camps, J; Hospital, A;
> Gelpi, J; Orozco, M
> (http://www.pnas.org/content/104/3/796.abstract)
>
> and
>
> Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing
> Nucleic
> Acids Force Fields *J. Theor. Chem. Comput. 2009*
> Eva Fadrna, Nad’a Spackova, Joanna Sarzynska, Jaroslav Koca, Modesto
> Orozco,
> Thomas E. Cheatham, III, Tadeusz Kulinski and Jiri Sponer
> (http://pubs.acs.org/doi/abs/10.1021/ct900200k)
>
>
>
> HTH,
> kevin
>
>
> On Wed, May 12, 2010 at 11:46 AM, Alan <alanwilter.gmail.com> wrote:
>
> > Hi There,
> >
> > I believe is common sense that FF are improving over the time, from
> > united-atoms to all-atoms etc. (just see the series Amber94, 96, 98, 99,
> > 03,
> > 99SB, 99bsc and now 99ildn, did I miss any?).
> >
> > What I am looking for is a recent review on FF in general (not only for
> > Amber, but Charmm, Opls etc. would be nice). By recent I mean something
> not
> > older than 3 y would be interesting.
> >
> > Suggestions are very appreciated. Can be even those to be (certainly)
> > published.
> >
> > Thanks,
> >
> > Alan
> >
> > --
> > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> > Department of Biochemistry, University of Cambridge.
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -- - -
> HK
>
> -------------------------------------------------------
> Kevin Eduard Hauser
>
> The Department of Chemistry
>
> Stony Brook University
> Stony Brook, New York 11794
>
> (631) 913.3194
> (561) 635.1848
>
> 84hauser.gmail.com
> -------------------------------------------------------
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Wed May 12 2010 - 10:30:05 PDT
