1. Overview over LigandParametrization

LigandParameterization is a python package that provides a simple interface for parameterizing non-standard residues for use in molecular dynamics simulations using the AMBER force field. The package is designed to be easily extensible, and is built around a series of stages that can be easily added or removed from a parametrization pipeline.

The package is designed to be used in a modular fashion, with a set of pre-defined recipes that can be used to parametrize a ligand with a single command. More on these recipes can be found in the Parametrization Recipes: section of the documentation.