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Ligand Force Fields

Amber is designed to work with several simple types of force fields, although it is most commonly used with parametrizations developed by Peter Kollman and his co-workers and “descendents”. The traditional parametrization uses fixed partial charges, centered on atoms. For a full description of the force fields and how to load them, please read Chapter 3 of the Amber 2021 Reference Manual.

GAFF2 Force Fields (recommended)

    For a general force field, for organic molecules like ligands, the recommended force field is gaff2.

    Ref

RED Database

    This is a database of RESP charges and force field libraries for small molecules and biological molecular fragments.

    REDDB (Resp \ Esp charge Data Base) is maintained by P. Cieplak, F. Dupradeau and co-workers. (Hint: click on "List Projects"; "co-factor_biochemistry" has entries that are commonly requested by users.)

"How's that for maxed out?"

Last modified: Aug 27, 2021