This example input file shows how to produce a family of embedded coordinates using distance geometry that starts with regularized substructures. If metrization is desired, the appropriate lines should be uncommented. The names of the family of embedded coordinates will be ``dg full embed 1.pdb" through ``dg full embed 10.pdb". Although the ``dg_full_embed.inp" protocol contains some regularization of the coordinates, further regularization is required by the ``dgsa.inp" simulated annealing protocol.
Disulfide bonds and other covalent links should be treated in the same fashion as in the prior template generation. The removed covalent links are reintroduced as distance restraints.