Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb) (jupyter notebook)

Version 4 (latest)

• Version 4 (latest)
  
• Version 3
  
• Version 2
  
• Version 1 (earliest)
  

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Ibuprofen small compound (3-letter code IBP, Drugbank code DB01050), a non-steroidal anti-inflammatory drug (NSAID) derived from propionic acid and it is considered the first of the propionics.

OpenBabel and ACPype packages are used to add hydrogens, energetically minimize the structure, and generate parameters for the GROMACS package. With Generalized Amber Force Field (GAFF) forcefield and AM1-BCC charges.

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliary libraries used are nb_conda_kernels, nglview, and ipywidgets. Environment setup can be carried out using the environment.yml in the code repository.