CHARMM-GUI supports the Amber force fields

Jumin Lee; Manuel Hitzenberger; Manuel Rieger; Nathan R. Kern; Martin Zacharias; Wonpil Im

doi:10.1063/5.0012280

CHARMM-GUI supports the Amber force fields

Jumin Lee, Manuel Hitzenberger, Manuel Rieger, Nathan R. Kern, Martin Zacharias, Wonpil Im

Publikation: Beitrag in Fachzeitschrift › Artikel › Begutachtung

194 Zitate (Scopus)

Abstract

As part of our ongoing efforts to support diverse force fields and simulation programs in CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI workflow. The currently supported Amber force fields are ff14SB/ff19SB (protein), Bsc1 (DNA), OL3 (RNA), GLYCAM06 (carbohydrate), Lipid17 (lipid), GAFF/GAFF2 (small molecule), TIP3P/TIP4P-EW/OPC (water), and 12-6-4 ions, and more will be added if necessary. The robustness and usefulness of this new CHARMM-GUI extension are demonstrated by two exemplary systems: a protein/N-glycan/ligand/membrane system and a protein/DNA/RNA system. Currently, CHARMM-GUI supports the Amber force fields only for the Amber program, but we will expand the FF-Converter functionality to support other simulation programs that support the Amber force fields.

Originalsprache	Englisch
Aufsatznummer	035103
Fachzeitschrift	Journal of Chemical Physics
Jahrgang	153
Ausgabenummer	3
DOIs	https://doi.org/10.1063/5.0012280
Publikationsstatus	Veröffentlicht - 21 Juli 2020
Extern publiziert	Ja

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title = "CHARMM-GUI supports the Amber force fields",

abstract = "As part of our ongoing efforts to support diverse force fields and simulation programs in CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI workflow. The currently supported Amber force fields are ff14SB/ff19SB (protein), Bsc1 (DNA), OL3 (RNA), GLYCAM06 (carbohydrate), Lipid17 (lipid), GAFF/GAFF2 (small molecule), TIP3P/TIP4P-EW/OPC (water), and 12-6-4 ions, and more will be added if necessary. The robustness and usefulness of this new CHARMM-GUI extension are demonstrated by two exemplary systems: a protein/N-glycan/ligand/membrane system and a protein/DNA/RNA system. Currently, CHARMM-GUI supports the Amber force fields only for the Amber program, but we will expand the FF-Converter functionality to support other simulation programs that support the Amber force fields.",

author = "Jumin Lee and Manuel Hitzenberger and Manuel Rieger and Kern, {Nathan R.} and Martin Zacharias and Wonpil Im",

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AU - Lee, Jumin

AU - Hitzenberger, Manuel

AU - Rieger, Manuel

AU - Kern, Nathan R.

AU - Zacharias, Martin

AU - Im, Wonpil

PY - 2020/7/21

Y1 - 2020/7/21

N2 - As part of our ongoing efforts to support diverse force fields and simulation programs in CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI workflow. The currently supported Amber force fields are ff14SB/ff19SB (protein), Bsc1 (DNA), OL3 (RNA), GLYCAM06 (carbohydrate), Lipid17 (lipid), GAFF/GAFF2 (small molecule), TIP3P/TIP4P-EW/OPC (water), and 12-6-4 ions, and more will be added if necessary. The robustness and usefulness of this new CHARMM-GUI extension are demonstrated by two exemplary systems: a protein/N-glycan/ligand/membrane system and a protein/DNA/RNA system. Currently, CHARMM-GUI supports the Amber force fields only for the Amber program, but we will expand the FF-Converter functionality to support other simulation programs that support the Amber force fields.

AB - As part of our ongoing efforts to support diverse force fields and simulation programs in CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI workflow. The currently supported Amber force fields are ff14SB/ff19SB (protein), Bsc1 (DNA), OL3 (RNA), GLYCAM06 (carbohydrate), Lipid17 (lipid), GAFF/GAFF2 (small molecule), TIP3P/TIP4P-EW/OPC (water), and 12-6-4 ions, and more will be added if necessary. The robustness and usefulness of this new CHARMM-GUI extension are demonstrated by two exemplary systems: a protein/N-glycan/ligand/membrane system and a protein/DNA/RNA system. Currently, CHARMM-GUI supports the Amber force fields only for the Amber program, but we will expand the FF-Converter functionality to support other simulation programs that support the Amber force fields.

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CHARMM-GUI supports the Amber force fields

Abstract

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