• Assign contact restraints: You can use this file to specify contacts between two atoms from residue i and j. The file should take the following format. A contact is defined as two atoms that are within 8 Angstroms of each other.

    "Res_No.i   Atom_type_i    Res_No.j   Atom_type_j   Weight"

    33   CA    6  CA 0.5
    60   CB   29  CB 5.0
    37   CB  345  CB 1.0
    109  CA   42  CB 2.0

    The first and third positions in the file specify the residue indices for residue i and j, respectively, while the second and fourth positions specify the atom types from residues i and j, respectively, to enforce the contact restraint for. Here, contact restraints may be enforced between CA or CB atoms. The final position specifies the weight to apply to the restraint.

    The weight for each constraint can be set to increase the likilihood that it will be satisfied.

    Here is an example of the restaint file.