Intermediate Tutorials for Standard MD

TUTORIAL B3: Case Study - Folding TRP Cage (Advanced analysis and clustering)

This tutorial is designed as a case study that will show you how to reproduce the work discussed in the following paper:
Simmerling, C., Strockbine, B., Roitberg, A.E., J. Am. Chem. Soc., 2002, 124, 11258-11259 ( http://dx.doi.org/10.1021/ja0273851)
It is a fairly long and in-depth tutorial covering creating structures using XLeap followed by running heating and long MD simulations to conduct protein folding experiments. It then moves on to more advanced analysis, including RMSD fitting, mdcrd to binpos conversion, average structure calculation, hydrogen bond analysis and dihedral angle tracking using ptraj. We also look at cluster analysis using the MMTSB toolset. It is recommended that you complete the Introductory tutorials before attempting this more advanced tutorial.

By Ross Walker

TUTORIAL A8: Loop dynamics of the HIV-1 integrase core domain

This tutorial is a walk-through of one of Prof Matt Lee's research projects. It will take you through how to set up, run, and analyze a simulation of the core domain of the HIV-1 integrase enzyme. (Japanese translation)

By Matt Lee