Journal article
Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field
Journal of chemical theory and computation, Vol.17(4), pp.2323-2341
04/13/2021
DOI: 10.1021/acs.jctc.0c01286
PMID: 33769814
Abstract
Computational protein design, ab initio protein/RNA folding, and protein–ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the nonlinear and linearized versions of the Poisson–Boltzmann equation (PBE), the domain-decomposition conductor-like screening model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatics models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least-squares style target function based on a library of 103 small-molecule solvation free energy differences. Mean signed errors for the adaptive Poisson–Boltzmann solver (APBS), ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.58 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields opens the door to their use for folding and design applications.
Details
- Title: Subtitle
- Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field
- Creators
- Rae A Corrigan - University of IowaGuowei Qi - University of IowaAndrew C Thiel - University of IowaJack R Lynn - University of IowaBrandon D Walker - University of Texas at AustinThomas L Casavant - University of IowaLouis Lagardere - Université Paris CitéJean-Philip Piquemal - Department of ChemistryJay W Ponder - Washington University in St. LouisPengyu Ren - University of Texas at AustinMichael J Schnieders - University of Iowa
- Resource Type
- Journal article
- Publication Details
- Journal of chemical theory and computation, Vol.17(4), pp.2323-2341
- DOI
- 10.1021/acs.jctc.0c01286
- PMID
- 33769814
- NLM abbreviation
- J Chem Theory Comput
- ISSN
- 1549-9618
- eISSN
- 1549-9626
- Publisher
- American Chemical Society
- Grant note
- DOI: 10.13039/100000055, name: National Institute on Deafness and Other Communication Disorders, award: R01DC012049; DOI: 10.13039/100000165, name: Division of Chemistry, award: 1751688; DOI: 10.13039/100000062, name: National Institute of Diabetes and Digestive and Kidney Diseases, award: R01DK110023; DOI: 10.13039/100000082, name: Division of Graduate Education, award: 1945994; DOI: 10.13039/100000057, name: National Institute of General Medical Sciences, award: R01GM106137, R01GM114237; DOI: 10.13039/100010663, name: H2020 European Research Council, award: 810367
- Language
- English
- Date published
- 04/13/2021
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Iowa Technology Institute; Biochemistry and Molecular Biology; Chemical and Biochemical Engineering
- Record Identifier
- 9984196999202771
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