Automate small-molecule parameterization from SMILES to GAFF2 and GROMACS topologies.
npx skills add https://github.com/BioKT/Skills-BIOKT --skill amber-parameterize
Please help me install this Agent Skill. Skill: amber-parameterize Source: https://github.com/BioKT/Skills-BIOKT/tree/main/amber-parameterize Command: npx skills add https://github.com/BioKT/Skills-BIOKT --skill amber-parameterize
Parameterize small molecules for MD simulations by deriving GAFF/GAFF2 parameters and topology from SMILES, generating AM1-BCC charges, and preparing Amber and GROMACS-ready files through a complete, reproducible workflow.
Run python parameterize.py 'SMILES_STRING' [OUTDIR] [MOLNAME] [CHARGE] to generate GROMACS-ready topologies and Amber parameters.
High-intent search queries and answers about installing and using this skill.
SMILES parameterization converts a molecular identifier into GAFF2 parameters and GROMACS-ready topologies. The workflow automates 3D generation, AM1-BCC charge assignment, frcmod creation, and acpype topology conversion.
Yes, GAFF parameterization requires Open Babel and AmberTools (antechamber, parmchk2, tleap) along with acpype in your PATH. These dependencies execute the 3D generation, typing, charge calculation, and topology conversion steps.
Automating ligand parameterization uses a Python script to reproduce the workflow. Running parameterize.py with a SMILES string, output directory, molecule name, and charge generates Amber and GROMACS files reproducibly.
Yes, antechamber assigns AM1-BCC charges and parmchk2 creates the frcmod file for novel ligands. The workflow handles GAFF2 atom typing and passes these parameters to tleap for topology generation.
Topology conversion fails when Open Babel, AmberTools, or acpype are missing from PATH, or when the input SMILES string is invalid. Ensure all dependencies are installed and the SMILES represents a valid chemical structure.
Acpype converts Amber topology files into GROMACS format by translating tleap-generated parameter files. This step produces GROMACS-ready topologies, completing the transition from SMILES through GAFF2 parameterization to the final simulation format.
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Hello-QMGenerate GAFF/GA2 parameterizations and AM1-BCC or RESP charges for AMBER/LAMMPS ligands.
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