Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb and Jupyter Notebook)
Version 1

Stable

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

help Creators and Submitter
Creator
Submitter
Activity

Views: 70   Downloads: 0

Created: 9th Sep 2020 at 10:51

Last updated: 14th Sep 2020 at 12:09

Last used: 20th Oct 2020 at 14:17

help Tags

This item has not yet been tagged.

help Attributions

None

Related items

Powered by
(v.1.11.master)
Copyright © 2008 - 2020 The University of Manchester and HITS gGmbH