how to set up a protein simulation

review

This workshop was held at the Unilever Centre for Molecular Informatics, in the Department of Chemistry, University of Cambridge on 17th November 2006. The course was run by Syma Khalid (University of Oxford) and Frank Beierlein (University of Southampton.)

The workshop was aimed at new PhD students and researchers new to biomolecular simulation techniques. The workshop consisted of a mixture of short lectures and 'hands-on' practical sessions providing a step-by-step guide to setting up protein simulations. Topics covered included: downloading a pdb and visualisation; adding missing residues; deciding upon ionisation states; solvating and adding counter-ions; equilibration; and carrying out a production run.

By popular demand, this workshop was re-run in April 2008 and we aim to re-run the workshop again in 2010.

downloads

Documentation from the course is available for download. To download the overall presentation and instructions, click here; for the presentation on using WHAT IF to assign ionisation states, click here; and to download all the example files needed, click here.

To be able to follow the course notes you will need access to the following software packages: VMD, WHAT IF, Modeller and Gromacs.

showcase talk

The day ended with a 'showcase' talk by Mark Sansom (University of Oxford) which highlighted the types of information which can be gained from protein simulations.

This presentation can be downloaded here.