CHARMM-GUI supports the Amber force fields
| Autor: | Nathan R. Kern, Martin Zacharias, Manuel Hitzenberger, Wonpil Im, Manuel Rieger, Jumin Lee |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
010304 chemical physics
Computer science Protein Conformation General Physics and Astronomy A protein Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences 0104 chemical sciences Computational science Molecular dynamics 0103 physical sciences Physical and Theoretical Chemistry Software |
| Zdroj: | The Journal of chemical physics. 153(3) |
| ISSN: | 1089-7690 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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