![]() Molecular dynamics based conformational sampling is achieved by heating a given structure to high temperature, then cooling random high temperature snapshots very gradually to a low temperature plateau. An example set of such functions is shown below: The force field used by Sander during conformational sampling is a set of equilibrium functions that describe bond, bond angles, electrostatic and other non-covalent interactions based on classical (Newtonian) physics derivations. Sander is used for energy minimization and conformational sampling. Additionally, Antechamber assigns atom types based on the user selected force field. It allows the conversion of various file types, as well as the generation of Amber prep files using restrained electrostatic potential charge (RESP) fitting for LEaP. This data is used to elucidate experimental measurements by calculating the prevailing conformational arrangements of biomolecular ions in the gas phase.Īntechamber is used as a preparatory tool for LEaP. Our group uses various facets of this suite such as LEaP, antechamber, and sander for building, minimization and conformational sampling of structures of empirically studied biomolecular ions (lipids, nucleotides, natural products). ![]() AMBER 9.0, 10.0 (University of California, San Francisco)ĪMBER is a Unix-based suite of programs designed for efficient structure building and molecular dynamics. ![]()
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