The evolution of the Amber additive protein force field: History, current status, and future
Abstract
Molecular dynamics simulations are pivotal in elucidating the intricate properties of biological molecules. Nonetheless, the reliability of their outcomes hinges on the precision of the molecular force field utilized. In this perspective, we present a comprehensive review of the developmental trajectory of the Amber additive protein force field, delving into researchers’ persistent quest for higher precision force fields and the prevailing challenges. We detail the parameterization process of the Amber protein force fields, emphasizing the specific improvements and retained features in each version compared to their predecessors. Furthermore, we discuss the challenges that current force fields encounter in balancing the interactions of protein–protein, protein–water, and water–water in molecular dynamics simulations, as well as potential solutions to overcome these issues.
Article Details
Journal Info
The Journal of Chemical Physics
American Institute of Physics
Authors (6)
Xianwei Wang
State Key Laboratory of Environmental Chemistry and Eco-toxicology, Research Center for Eco-environmental Sciences
Danyang Xiong
Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University 2 , Shanghai 200062,
Yueqing Zhang
Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University 2 , Shanghai 200062,
Jihang Zhai
Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University 2 , Shanghai 200062,
Yu-Cheng Gu
Syngenta
Xiao He