Examples


Test Case: Dekapeptide

  • Sequence: PQITLWQRPL
  • Structure: peptide.pdb


    Creating Peptide Bonds

    Create the peptide bonds among the 10 residues.


    Creating New Atoms

    Use GSDG algorithm for placing atoms without coordinates (e.g. hydrogens on x-ray structures).


    Minimize the Potential Energy

    Minimize the potential energy of the peptide using conjugate gradient minimization.


    Molecular Dynamics

    Run 5 ps of molecular dynamics. Output the energies and a structure every 1 ps.