Distance Geometry

The example input file below shows how to produce a family of embedded substructures using distance geometry. The substructures are regularized after embedding using minimization against the DG energy term. The substructure selection depends on the type of macromolecule. The example file has been tested for proteins and nucleic acids.

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.

It is important for the subsequent regularization protocol that each residue of the macromolecule (as defined by atom tags, see Section 2.15) contain at least three atoms. Otherwise, the template fitting to generate the missing atoms will be ill-behaved. The filenames of the family of embedded substructures are “dg sub embed 1.pdb" through “dg sub embed 10.pdb".

dg_sub_embed.inp