Summary

Jupyter Notebook containing a tutorial 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 Sulfasalazine protein (3-letter code SAS), used to treat rheumatoid arthritis, ulcerative colitis, and Crohn's disease.

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.

Parameters

Inputs:

• ligandCode: 3-letter code of the ligand structure (e.g. IBP)

• mol_charge: Molecule net charge (e.g. -1)

• pH: Acidity or alkalinity for the small molecule. Hydrogen atoms will be added according to this pH. (e.g. 7.4)

Outputs

• IBPparams.gro: Structure of the parameterized ligand in gro (GROMACS) format.

• IBPparams.top: Topology of the parameterized ligand, including a reference to the IBPparams.itp.

• IBPparams.itp: Include Topology File (itp) of the parameterized ligand, including the parameters information: bonds, angles, dihedrals, etc.

Additional Resources

• Tutorial Page for this workflow

• GitHub repository

• View in Binder

• Documentation