This tutorial was designed to be a wholistic example, from RCSB structure to QSM calculations, of performing QM/MM through LICHEM.
Prerequisites
It is expected that you have a basic understanding of Python3 before using the tools in this tutorial. Previous experience with TINKER is a plus.
| Setup | Download files required for the lesson | |
| 00:00 | 1. Introduction |
What is LICHEM?
What is QM/MM? (FIXME) |
| 00:15 | 2. Structure Preparation |
How do I make a structure biologically relevant?
Do I need to add hydrogens? Where do parameters come from? How do I add ions and solvate a system? |
| 02:15 | 3. Molecular Dynamics and Clustering |
How do I perform a molecular dynamics simulation with AMBER?
What are some of the different approaches to clustering? How do I cluster a simulation based on specific criteria? How do I do subclustering? |
| 04:15 | 4. QM/MM Structure Preparation |
How is a Tinker XYZ file different from a regular XYZ file?
How do I convert a PDB file to a Tinker XYZ file? How do I write a Gaussian BASIS file? How do I use LICHEM for a single point energy calculation? |
| 06:15 | 5. DFP Optimizations and Strategies for Building a Suitable Product | ??? |
| 07:15 | 6. QSM: The Quantum String Method | ??? |
| 08:15 | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.