Hi Vlad,
amber99sb-nmr1-ildn comes from:
1. Li, .. Bueschweiler, Angewande Chemie Intl Edition 2010
2. Lindorff-Larsen..., Proteins 2010
That ff was shown to outperform many others in the paper I cited. Is this
the one you are using based on your discussion with the D.E. Shaw's group
member?
best,
Thomas
On 21 November 2012 17:35, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de>wrote:
> Hi Thomas,
>
> These are the NMR-based parameters I am referring to:
> Li, .. Bueschweiler, Angewande Chemie Intl Edition 2010
>
> The PLoS One paper by Shaw describes a different set of NMR-based force
> field modification of 99sb ....This set is though not available in the
> AMBER distribution ... Although the modification's spirit is similar, of
> course tests with very long simulations with the Brueschweiler
> modifications are still missing.
>
> Best
> Vlad
>
> On 11/21/2012 03:47 PM, Thomas Evangelidis wrote:
> > 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
>
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Received on Wed Nov 21 2012 - 08:00:03 PST
