Document Type
Article
Publication Date
9-11-2025
Keywords
Intrinsically disordered proteins, Molecular-dynamics simulations, coupling-constrants, quantum-mechanics, energy surfaces
Abstract
Developing accurate force fields for biomolecules remains a significant challenge due to the subtle energetic differences between various conformational states. We present a novel force field model for polyalanine, ALAMP2_25, developed using adaptive force matching (AFM) with M & oslash;ller-Plesset perturbation theory at the second order (MP2) as the reference method. By fitting smaller model compounds and transferring parameters to larger peptides, we overcome the limitations of traditional AFM approaches and enable the use of more accurate electronic structure methods. The ALAMP2_25 model incorporates a new correction scheme, Smooth Fourier Transform-based phi, psi correction map (SFT-CMAP), which efficiently describes phi, psi coupling with reduced overfitting. Our model demonstrates good agreement with experimental J-coupling data for hydrated polyalanine and shows improved transferability to N-methylated cyclic alanine when compared to previously reported DFT based models. The developed framework provides a pathway for creating accurate force fields for a broader range of amino acids and biomolecules, enabling first-principles-based simulations of complex biological systems with applications in protein folding, ligand binding, and drug design.
Citation
Ying Yuan, Feng Wang; An Adaptive Force Matching Potential for Alanine Developed with Møller–Plesset Perturbation Theory and Smooth Fourier Transform Correction Map. J. Phys. Chem. B 11 September 2025; 129 (36): 9165–9174. https://doi.org/10.1021/acs.jpcb.5c04529
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
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