DISUlfide [NBXMod int] NCYST (I5) IRES,JRES (2I5) repeated NCYST times
This command requires formatted (not free field) input following the DISULFIDE line.
The first line following the command gives the number of cystine cross bridges to be made; The lines following give the residue numbers (not residue identifiers) of the cysteines to be linked. The residue number of a residue is its position in the list of all residues in the structure including any special termini which have been added. The linkage process involves adding bonds, bond angles, torsion angles, and non-bonded exclusions for the additional bond. The NBXMOD option controls the automatic generation of non-bonded exclusions, see Nbxmod, for more details.
An attempt has been made to ease the burden of going from residue identifiers to residue numbers which will be different for segments which have N-terminal residues added. Whenever the type of segment as specified in the READ SEQUENCE command is CHARMM explicit hydrogen or all hydrogen, the residue numbers will first be increased by one. If the two residues given are not cysteines, the residue numbers will be decremented by one, and the attempt repeated. If this fails, the command will die. Note that this does not help you if you have more than one segment in your structure.
When using disulphides, it is important that the sequences reference a cysteine residue which is intended to be joined. In an all atom topology file, see AMBER94RTF, there are two cysteine residues, one of which has a thiol and one of which has a sulfur.
It is not possible to bridge an atom in the primary space with that of a symmetric image using this command (see Images).