CCPBioSim MM-GBSA Workshop

This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.

This workshop walks through the process of perfprming a basic MM-GBSA analysis of a molecular dynamics simulation of a protein-ligand complex to estimate the ligand binding free energy. The approach here uses OpenMM with a little help from ParmEd.

This example uses data from a simulation performed using OpenMM, but could readily be adapted for use with simulations run with Amber or GROMACS (and maybe CHARMM).

How to Use

This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.

Pull the container from our repository::

docker pull ghcr.io/ccpbiosim/mm-gbsa-workshop:latest

In our containers we are using the JupyterHub default port 8888, so you should forward this port when deploying locally::

docker run -p 8888:8888 ghcr.io/ccpbiosim/mm-gbsa-workshop:latest

Authors

Workshop Content Authors:

• Charlie Laughton

Contact

Please direct all questions and feedback to Charlie Laughton