Next: Examining the Topology File Up: Topology Tutorial Previous: Required Programs

Getting Started

If you downloaded the tutorial from the web, the files that you will be needing can be found in a directory called topology-tutorial-files. If you received the files through a workshop, they can be found in the same directory under the path /Workshop/topology-tutorial.

Unix/Mac OS X Users: In a Terminal window type:

cd <path to topology-tutorial-files directory>

You can list the content of this directory, by using the command ls.
Windows Users: Navigate to the topology-tutorial-files directory using Windows Explorer.

This will place you in the directory containing all the necessary files. In the figure below, you can see the structure of this directory.

**Figure 1:** Directory Structure for tutorial excercises. Output for all simulations is provided in an ``example-output'' subdirectory within each folder shown.
$\begin{figure}\begin{center} \par \par \latex{ \includegraphics[scale=0.5]{pictures/directory-structure} } \end{center} \end{figure}$

In this section you will learn about typical situations in which you may need to create your own topology file for a given protein or biological molecule. You will learn about biological systems which utilize amino acids other than the ``naturally occurring" 20 and how you may simply be able to alter topology file entries to account for non-standard amino acids without needing to do any new parameterization.

Next: Examining the Topology File Up: Topology Tutorial Previous: Required Programs

tutorial-l@ks.uiuc.edu