Yes Thomas,
But in Lindorf et al 2012 , the best force field is not this one but is
ff99SB*-ILDN, in which the * stands for Best et al NMR-based
modifications from 2008.
Best,
Vlad
On 11/21/2012 04:46 PM, Thomas Evangelidis wrote:
> 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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--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Wed Nov 21 2012 - 08:00:03 PST
