thanks for interest in our ff19SB model. We haven't yet released the actual
CMAP files as we were waiting for feedback from reviewers first in case for
some reason the model needs adjusting. If people would like to beta-test
parameters, under the understanding that they may not be the final ff19SB
set and should not be used (yet) for production runs, please contact me off
list.
Indeed, the water model appears to be crucial. We obtain best agreement
with Onufriev's OPC water, though TIP4P-Ew and OPC3 perform notably better
than TIP3P. OPC has also been shown recently to do better for IDPs, so we
are hopeful about future tests of that combination.
Carlos
On Wed, Jun 19, 2019 at 12:35 PM Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Uhhh! That's good news...
>
> It seems ff19SB uses CMAPs, which (as far as I know) aren't implemented in
> the native parameter files of AMBER... hence, there should be some
> development work in progress...
>
> It also seems the water model is crucial for the good reproduction of NMR
> results, particularly ff19SB+TIP3P is worse than ff14SB+TIP3P (at least in
> some reported properties: Figs 9, S4, etc)...
>
> Yet, it is intriguing the over-estimation of ff19SB in the helical
> propensity of K19 peptide (Fig. 10), which aminoacids (A and K) are among
> the best correlated with NMR experiments (Figs. 7 and 9D).
>
> It would be interesting to see future application of ff19SB to IDPs...
>
> Thanks for the update.
>
> Best,
>
> Matias
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Nikolay N. Kuzmich" <nnkuzmich.gmail.com>
> Para: amber.ambermd.org
> Enviados: Miércoles, 19 de Junio 2019 5:46:39
> Asunto: [AMBER] ff19SB forcefield
>
> Dear Amber developers,
>
> yesterday I came across the article in ChemRxiv about the updated
> forcefield ff19SB
>
> https://chemrxiv.org/articles/ff19SB_Amino-Acid_Specific_Protein_Backbone_Parameters_Trained_Against_Quantum_Mechanics_Energy_Surfaces_in_Solution/8279681
> I am just curious when will it be available for simulations within the
> Amber/AmberTools package.
>
> Kind regards,
> Nick
>
> Laboratory of Drug Safety
> Research Institute of Influenza,
> WHO National Influenza Centre of Russia,
> 15/17 Professor Popov St.,
> Saint-Petersburg
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>
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Received on Wed Jun 19 2019 - 10:30:02 PDT
