Introduction

Often, one encounters the need in molecular dynamics to simulate molecules for which topology and parameter information does not exist. In many cases, parameter development is necessary, but in others it may not be. This tutorial introduces how to create this information based on existing topology information for other molecules, without the need for new parameter development.

The tutorial is subdivided in three sections. The first one introduces the method of topology file creation and situations when it is appropriate and inappropriate. The second section utilizes the method to create a topology file for a tripeptide bound to an enzyme and performs a simulation of the system. The last section provides the solution to a topology file creation problem posed in the tutorial.

Throughout the text, some material will be presented in separate ``boxes". Some of these boxes include complementary information to the tutorial, such as information about the biology of the molecules presented, and tips or warnings one should be aware of. These boxes are not required for understanding the tutorial and may be skipped if you are short on time, but this is not recommended.

Boxes with an exclamation sign are especially important and should not be skipped.

If you have any questions or comments on this tutorial, please email the TCB Tutorial mailing list at tutorial-l@ks.uiuc.edu. The mailing list is archived at http://www.ks.uiuc.edu/Training/Tutorials/mailing_list/tutorial-l/.