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AMBER Force Field - DOAJ

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Last Updated: 23 April 2022

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Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field

Using density functional theory, the data includes geometries in XYZ coordinate format for cluster models that were used to calculate proton transfer energies and derive bond parameters, as well as point charges for the force field. Also included are the final parameter files that can be used with the Amber software package to generate input files for molecular dynamics simulations. We developed a model that is embedded in a POPC lipid bilayer membrane and solved with TIP3P water molecules and counterions based on the high-resolution X-ray crystal structure of the ba3-type CcO from Thermus thermophilus.

Source link: https://doi.org/10.1016/j.dib.2016.07.043


Molecular Dynamics Simulations of CO2 Molecules in ZIF-11 Using Refined AMBER Force Field

Based on ab initio bonding energies of CO2–[C7H5N2] complexes, the AMBER force field's nonbonding parameters have been improved. In SIM II, the CO2 molecules are mostly embedded around and nearer to the hydrogen atom of imidazolate ring in SIM II than those found in SIM I. In a free flexible framework simulation, Zn-Zn and Zn-N RDFs test the effectiveness of changing AMBER bonding parameters. The results of a flexible framework simulation using enhanced nonbonding AMBER parameters in this report are not significantly different from those obtained in SIM II, due to the lack of computing resources and time in this study.

Source link: https://doi.org/10.1155/2013/415027

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