This post covers the essentials of how to set up a scan of different peptide conformations. We have used this method to calculate more than 1.5M QM calculation on model peptides in our group.

In this example we make a tri-glycine peptide and scan over the phi/psi torsion angles between -180 and 180 degrees with 60 degrees spacing.

For each conformation, the MMFF94 force field energy is printed and the structure is saved as an XYZ file.


from fragbuilder import Peptide

# Create a peptide object with the sequence
# glycine-glycine-glycine.
sequence = "GGG"
pep = Peptide(sequence)

# Define a list of angles.
angles = range(-180, 180, 60)

# Double loop over phi/psi angles in the desired range.
for psi in angles:
  for phi in angles:

    # Set the second (leucine) residue to (phi, psi).
    pep.set_bb_angles(2, [phi, psi])

    # Print the energy of the peptide in this state.
    # This is of course just an example.
    print pep.get_energy()

    # Save each conformation.
    pep.write_xyz("pep_%04i_%04i.xyz" % (phi, psi))