I think I found the reference I was looking for:
[1] Klepeis, J. L., Lindorff-Larsen, K., Dror, R. O., and Shaw, D. E.
Long-timescale molecular dynamics simulations of protein structure and
function. Current Opinion in Structural Biology 19, 2 (Apr. 2009), 120–127.
Alan
On Wed, May 12, 2010 at 18:04, Alan <alanwilter.gmail.com> wrote:
> 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<<
>
--
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 Thu May 13 2010 - 09:30:06 PDT
