links

A links directive is used to specify the addition of a covalent bond between two atoms. The syntax for specifying a link is as follows:

<chain1>_<resi1>_<atom1>-<chain2>_<resi2>_<atom2>

<chain1> and <chain2> are the chain IDs, <resi1> and <resi2> are the residue numbers of the two residues that form the link, and <atom1> and <atom2> are the atom names of the two atoms that form the link. For example, A-12_O-C_15_N would create a covalent bond between the oxygen atom of residue 12 in chain A and the nitrogen atom of residue 15 in chain C. You can use either 1-byte or 3-byte residue names.

Links are not normally needed in a mods directive of a psfgen task. However, if you are using a non-published pdb file that does not include metadata indicating non-protein bonds (e.g., a covalent bond between a glycan monomer and a protein), you can use the links directive to specify each required bond. The links directive is not needed for standard protein structures.