Assignment5

Assignment 5

1. Build a small dipeptide such as: [|atest.png]

Use the GMMX option in Pcmodel to do a conformational search on all the rotatable bonds (do not include amides and esters). Record the energy and dipole moments of the five lowest energy conformers.

Submit each of the five lowest energy conformers to a MO calculation: B3LYP/6-31G*, gas phase, solvent THF, solvent water. Record the energies and dipole moments from each calculation.

Does the order of the conformational energies change as a function of the type of calculation?

2. Download and install a copy of AmberTools. Prepare the ligands in the attached file for use with Amber or Dock. (You can check your work using Chimera ). [|ligand_test.mol2]