README.md

NAMD-MD

This repository tries to introduce molecular dynamics of the protein-ligand complex to more people, especially those beginners, with all open-sourced resources.

• VMD (https://www.ks.uiuc.edu/),
• NAMD (https://www.ks.uiuc.edu/) and
• py3Dmol (https://github.com/avirshup/py3dmol)
• Open babel (https://github.com/openbabel/openbabel)
• Charmm as per https://www.charmm.org/charmm/resources/charmm-force-fields/ for protein
• LigPargen (http://zarbi.chem.yale.edu/ligpargen/).

Usage

There are two ways you could use this workflow,

1. Run this procedure on Colab directly where all dependencies are installed on the fly each time you use it

2. Locally use after installing all dependencies by yourself.