ArticleJournal of chemical theory and computation2014
ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins.
Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 114 citations in OpenAlex.
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- NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins.Chemical reviews · 2022Review
- Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field.The journal of physical chemistry. A · 2022Article
- CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.Journal of computational chemistry · 2022Article
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- Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.Journal of chemical theory and computation · 2021Article
- Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds.Physical chemistry chemical physics : PCCP · 2021Article
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- Development and Validation of a DFT-Based Force Field for a Hydrated Homoalanine Polypeptide.The journal of physical chemistry. B · 2021Article
- SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations.Journal of computer-aided molecular design · 2021Article
- A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.The Journal of chemical physics · 2020Article
- Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method.Journal of chemical theory and computation · 2020Article
- ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.Journal of chemical theory and computation · 2020Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.