To model a peptide using the ICM Biased Probability Monte Carlo method:

• MolMechanics/Sample Peptide
• Enter a name for the simulation.
• Enter the one letter amino acid code for the peptide.
• Choose whether the peptide is cyclic or not.
• Determine the state of the N-terminus and C-terminus.
• Add a value for the effort. This represents the length of the simulation - values between 1 and 10 will give a thorough sampling. A larger effort value will be needed for longer peptides.
• When the simulation is finished a stack of conformations will be displayed in the ICM workspace.