Course Description and Information

This is a laboratory-based course designed to teach the fundamental principles of molecular mechanics programs, and to develop practical skills in using these programs to investigate structure-function relationships in macromolecular systems.

Syllabus and Course Schedule

Insight Tutorial 1: Basic Commands

Insight Tutorial 2: Investigating Molecular Structure (Proteins)

Insight Tutorial 2: Investigating Molecular Structure (tRNA)

Building Proteins Tutorial

Protein.pdb (for Building Proteins Tutorial)

Nucleic Acid Loop Building Tutorial

Loop.pdb (for Loop Building Tutorial)

Homology Modeling Tutorial

Tutorial

Modeller 6 Sample Files

alignment.ali

model-default.top

haptoglobinB.doc

The principal software packages for this course are VMD (a molecular graphics program) and NAMD (a molecular simulation program). Both packages are very widely used and are available without charge. They can be downloaded from the website of the Theoretical and Computational Biology Group at the University of Illinois at Urbana/Champaign. We are indebted to Dr. Klaus Schulten, the Director of that group, for allowing us to post pdf files containing the user’s guides and tutorials for VMD and NAMD.

 

VMD User's Guide

VMD Tutorial

NAMD User's Guide

NAMD Tutorial

Unix Basic Commands

Unix Tutorial