Fig. 5: Fine-tuning torsion parameters of Glutamine in amber ff99SBws-STQ. | Nature Communications

Fig. 5: Fine-tuning torsion parameters of Glutamine in amber ff99SBws-STQ.

From: Optimized protein-water interactions and torsional refinements yield balanced atomistic protein force fields

Fig. 5

A Residual helix fraction of H16, simulated with three amber ff99SBws-based force fields: ff99SBws, ff99SBws-STQ, and ff99SBws-STQ′ (kψ (Q) = 1.5 kJ/mol). NMR-derived results are taken from Urbanek et al.114,115. B Residual helix fraction of (AAQAA)3 as a function of temperature simulated with ff99SBws and ff99SBws-STQ′. The inset shows the temperature-dependent helix fraction. Mean helix fractions and associated standard errors were estimated by block averaging over five equal-length blocks of the trajectory. Source data are provided as a Source data file.

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