Preparing to run biomolecular QM/MM simulations with CP2K using AmberTools

By combining the accuracy of quantum mechanics (QM) and the speed of molecular mechanics (MM) they enable studying specific properties beyond the reach of those methods in isolation (such as photochemical effects, ligand binding, reactivity, and a long et cetera). However, the preparation of such simulations can be difficult and tedious. Additionally, subtle changes in the setup process can often affect the accuracy and robustness of the results. This course aims to showcase a consistent protocol to set up your system in order to run QM/MM simulations using CP2K.

This course covers basic tools and technologies needed to succeed in setting up a QM/MM simulation with the AmberTools suite, and will be run with hands-on exercises. It provides a background to the preparation of biological systems for molecular modelling and offers practical experience in creating topologies successfully and running simple QM/MM simulations with CP2K in a HPC environment (ARCHER). You will learn about the intricacies behind the molecular modelling of biological systems, such as the practical skills required to handling and preparing PDB files to create ready-for-use topologies in CP2K.

At the end of this session you will be able to …

This online course consists of an interactive hands-on practical session presented remotely using Collaborate. Attendees will be given access to ARCHER to execute the practical exercises.

The duration of the sessions will be between 2 and 3 hours, depending on the level of interactivity.

Technical requirements:

Trainers:

Prerequisites

In this lesson we use AmberTools remotely on ARCHER. The following is expected:

  • Comfortable using the Linux command line.
  • Prior experience with HPC computing or QM/MM knowledge are not required.

This online course is a collaboration between ARCHER2 Training and BioExcel.

Schedule

Setup Download files required for the lesson
00:00 1. Overview of AmberTools20 What is the AmberTools package?
00:05 2. Log in and environment set up in ARCHER How do I access ARCHER?
How do I set up the correct environment in ARCHER?
00:10 3. Preparing your PDB file What should I check before preparing a simulation?
00:25 4. Parameterising your ligands How do I generate parameters for non-conventional residues?
00:40 5. System set up How do I create topology and coordinate files?
00:50 6. Energy minimisation What should I do after generating my system’s topology and coordinates?
How do I refine and remove bad contacts from the initial structure?
01:00 7. Thermalisation and Density equilibration How do I equilibrate my system with sander?
01:20 8. Adding missing LJ parameters and recentering coordinates Does the MM forcefield have all the parameters to run a QM/MM simulation?
How do I modify an Amber topology?
01:30 9. QM/MM monitorisation runs What is CP2K?
What is the first step of a QM/MM simulation?
01:55 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.