Connecting two minima with a pathway

There are two versions of this tutorial, one for AMBER users, using A9OPTIM, and one for CHARMM users, using COPTIM.

AMBER (A9OPTIM) version

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

CHARMM (COPTIM) version

This tutorial takes two structures for the met-enkephalin neurotransmitter peptide, generated using GMIN, and runs through setting up how to connect them with a connected pathway of minima and transition states using OPTIM and CHARMM (COPTIM).

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