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
>
>
> 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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>>
>
>
--
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 - 08:00:02 PST
