automodel.special_patches() -- add additional patches to the topology

special_patches(aln)

This routine, which is usually empty, can be redefined by the user to make additional changes to the model topology, such as:

• adding patches by calling model.patch(), such as user-defined disulfides (see Section 2.2.7 for an example)

• renumbering the residues or renaming the chains (see Section 2.2.13 for an example)

• changing CHARMM atom types, by assigning to Atom.type or by calling automodel.guess_atom_types()