The guidelines given in this tutorial are intentionally very loose. To prepare for this tutorial, read the InsightII Discover notes.

Part 1: Getting Started

1. Start InsightII, select the Discover module, and spend a few minutes browsing through the menus to familiarize yourself with the options.

Part 2: Building an Extended Peptide

1. Build a 14 residue peptide in an extended conformation. This tutorial will work best if you do not have any Gly or Pro residues in your structure.
2. Save this model.

Part 3: Energy Minimization With No Restraints

1. Select the Discover Module and energy minimize your starting structure.
   Use no Restraints.
   Select the Parameters/Minimize menu.
   Use the Conjugate Gradients minimizer, a maximum of 500 iterations or a minimum derivative of 0.1, and with no cross terms, morse term, or charges.
   Select the Run/Run menu and run your minimization on your local workstation.
2. Save your minimized structure using a new file name.

Part 4: Minimization to an Alpha Helix Conformation

1. Restore your starting structure.
2. Minimize the peptide into an alpha helical conformation in a series of steps by specifying H-bonding restraints appropriate for an alpha helix. It is realistic to restrain H-bonds in the range 1.8-2.0 Angstroms (the hydrogen to hydrogen-bond-acceptor distance).
   In the first step, specify restraints corresponding to only the first turn of helix. Then minimize.
   In the next step, include restraints for the first two turns, then minimize, etc.
3. Save your final minimized structure in a file named min_helix.psv in your home directory.

Part 5: Minimization with Discover_3

1. Recall the structure saved at the end of Part 2.
2. Select the Discover_3 module.
3. Setup your system. Don't select PBC_on or modes.
4. Browse through the Specify pull-down menus.
5. Select the Calculate/Minimize menu. Select the more option..
6. Review the options in this menu; modify parameters as you find necessary. Then Execute this menu.
7. Click on D_Run/Run and run your calculation.
8. Review the output file and verify that the structure is minimized.
9. Save your final minimized structure in a file named discover_3.psv in your home directory.

Part 6: Verify that you have completed this portion of the assignment.