Hi Albert,
If I am guessing right, Vlad refers to the Amber99sb-nmr1-ildn or
Amber99sb-phi-ildn, which have been shown to outperform multiple other ffs
in a wide variety of systems, many of which included small peptides.
However, I don't think it would be of interest to you since the simulations
they ran for validation were not long. This is the paper:
Beauchamp KA, Lin YS, Das R, Pande VS., "Are Protein Force Fields Getting
Better? A Systematic Benchmark on 524 Diverse NMR Measurements.", J Chem
Theory Comput. 2012 Apr 10;8(4):1409-1414. Epub 2012 Mar 12.
best,
Thomas
On 21 November 2012 16:36, Albert <mailmd2011.gmail.com> wrote:
> Hi Vlad:
>
> thanks a lot for such kind comments again.
>
> I've read that PLOS ONE paper before, in that paper, the author from
> Deshaw group finnally conclude that the CHARMM22star and Amber99ILDN are
> the two best FF for long time scaled MD simulation. However, my system
> is a membrane/protein one, and I've asked people in charge of
> CHARMM22star FF, and he told me that they didn't validate the
> compability between CHARMM22star and CHARMM36_lipids FF. Of course for
> Amber FF, I hope it won't be a problem for the compability between
> AMBER99SB-ILDN and AmberGAFF FF.
>
> If am right, both AMBER99SB-ILDN and CHARMM22star FF were devoloped
> in Deshaw group instead of AMBER or CHARMM group.
>
>
> best
> Albert
>
> On 11/21/2012 03:21 PM, Vlad Cojocaru wrote:
> > See also
> >
> > Lange, Spoel and de Groot, Biophys. J. 2010
> >
> > From the NMR-based modifications, see
> > Li, .. Bueschweiler, Angewande Chemie Intl Edition 2010
> >
> > Also, ff12SB could be interesting to follow but it is not published yet
> > ... However, on this list people have reported successful long
> > simulations ...
> >
> > Best wishes
> > Vlad
>
>
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>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Nov 21 2012 - 07:00:03 PST
