Balancing simulation accuracy and efficiency with the Amber united atom force field

The Journal of Physical Chemistry. B
Meng-Juei Hsieh, Ray Luo

Abstract

We have analyzed the quality of a recently proposed Amber united-atom model and its overall efficiency in ab initio folding and thermodynamic sampling of two stable beta-hairpins. It is found that the mean backbone structures are quite consistent between the simulations in the united-atom and its corresponding all-atom models in Amber. More importantly, the simulated beta turns are also consistent between the two models. Finally, the chemical shifts on H alpha are highly consistent between simulations in the two models, although the simulated chemical shifts are lower than experiment, indicating less structured peptides, probably due to the omission of the hydrophobic term in the simulations. More interestingly, the stabilities of both beta-hairpins at room temperature are similar to those derived from the NMR measurement, whether the united-atom or the all-atom model is used. Detailed analysis shows high percentages of backbone torsion angles within the beta region and high percentages of native contacts. Given the reasonable quality of the united-atom model with respect to experimental data, we have further studied the simulation efficiency of the united-atom model over the all-atom model. Our data shows that the united-atom ...Continue Reading

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Citations

Apr 8, 2011·Journal of Biomolecular Structure & Dynamics·Vinod JaniRajendra Joshi
Apr 9, 2013·Journal of Chemical Theory and Computation·Hai NguyenCarlos Simmerling
Aug 11, 2018·Journal of Chemical Information and Modeling·Bianca VillavicencioHugo Verli

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