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ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

[Image: see text] We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed t...

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Autores principales: Cerutti, David S., Swope, William C., Rice, Julia E., Case, David A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2014
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196740/
https://www.ncbi.nlm.nih.gov/pubmed/25328495
http://dx.doi.org/10.1021/ct500643c
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author Cerutti, David S.
Swope, William C.
Rice, Julia E.
Case, David A.
author_facet Cerutti, David S.
Swope, William C.
Rice, Julia E.
Case, David A.
author_sort Cerutti, David S.
collection PubMed
description [Image: see text] We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard–Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields.
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spelling pubmed-41967402015-09-18 ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins Cerutti, David S. Swope, William C. Rice, Julia E. Case, David A. J Chem Theory Comput [Image: see text] We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard–Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields. American Chemical Society 2014-09-18 2014-10-14 /pmc/articles/PMC4196740/ /pubmed/25328495 http://dx.doi.org/10.1021/ct500643c Text en Copyright © 2014 American Chemical Society Terms of Use (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html)
spellingShingle Cerutti, David S.
Swope, William C.
Rice, Julia E.
Case, David A.
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
title ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
title_full ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
title_fullStr ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
title_full_unstemmed ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
title_short ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
title_sort ff14ipq: a self-consistent force field for condensed-phase simulations of proteins
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4196740/
https://www.ncbi.nlm.nih.gov/pubmed/25328495
http://dx.doi.org/10.1021/ct500643c
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