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.
| Note: to incorporate disulfide bonds - use numerical markers e.g. "C1VGPVC1" |