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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 19 2019 - 10:00:03 PDT
