Connecting two minima with a pathway

This tutorial takes two PDB structures for the ALA-PHE dipeptide (generated with LEaP and GMIN or from another source), and runs through setting up how to connect them with a connected pathway of minima and transition states using OPTIM and AMBER9 (A9OPTIM).

• Setting up
• Using GMIN to generate endpoints
• Finding an initial path with OPTIM and starting up PATHSAMPLE
• Alternatively, making the initial path with PATHSAMPLE itself
• Expanding the kinetic transition network with PATHSAMPLE