antechamber
A command-line tool in AmberTools for preparing small molecules or non-standard residues within GAFF/AMBER-compatible chemical space for molecular mechanics simulations, by automating atom/bond typing, charge generation or import, and force-field–compatible input generation. USE WHEN you are working in AMBER, dealing with molecules not covered by standard force fields, and already have a structure that can be processed (e.g., pdb, mol2, ac, gout). Typical use cases include parameterizing ligands or modified residues (assigning atom/bond types, generating or reading partial charges), converting structures from upstream tools into mol2/prepi formats, and preparing topology-ready inputs for downstream tools such as LEaP. DO NOT USE for standard residues, metal complexes, inorganic systems, or when no valid molecular structure is available (e.g., only SMILES).
Installation and usage
A command-line tool in AmberTools for preparing small molecules or non-standard residues within GAFF/AMBER-compatible chemical space for molecular mechanics simulations, by automating atom/bond typing, charge generation or import, and force-field–compatible input generation. USE WHEN you are working in AMBER, dealing with molecules not covered by standard force fields, and already have a structure that can be processed (e.g., pdb, mol2, ac, gout). Typical use cases include parameterizing ligands or modified residues (assigning atom/bond types, generating or reading partial charges), converting structures from upstream tools into mol2/prepi formats, and preparing topology-ready inputs for downstream tools such as LEaP. DO NOT USE for standard residues, metal complexes, inorganic systems, or when no valid molecular structure is available (e.g., only SMILES).
Depois de instalar, você pode usar esta skill executando o seguinte comando no terminal:
skills use antechamber