DNA-workshop

This workshop is a hands-on exercise to (a) setup a DNA + ligand simulation in explicit solvent; (b) run molecular dynamics using AMBER MD engine and (c) Visualise the trajectory using a viewer.

The workshop illustrates:

1. The use of jupyter-notebook (https://jupyter.org/)
2. The use of Python HTMD (https://software.acellera.com/docs/latest/htmd/index.html)
3. The use of Amber simulation (www.ambermd.org) and Ambertools
4. The use of nglviewer (www.nglviewer.org)
5. The use of Python MDtraj module (www.mdtraj.org)

Requirements

A basic knowledge of Nucleic Acids, Python and MD simulation methods

Training Material

A Jupyter notebook and associated data files

Contact

Please direct all comments and queries to Shozeb Haider (shozeb.haider@ucl.ac.uk)

dna-workshop