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First, add a 'patch' to the generate.inp script. This patch must include the following:
        name of the residue
        bond(s) to be made
        new angles resulting from bond formation
        new dihedrals resulting from bond formation.
Additionally, you must tell CNS between
what 2 residues the bond(s) should be formed.

The following is an example of the patches used to make a
covalent bond between OG of SER 125 and the phosphorous
atom of DEP 401:
 {* any special ligand patches can be applied here *}
   presidue DEP
      add bond 1OG 2P
      add angle 1CB 1OG 2P
      add angle 1OG 2P 2O1
      add angle 1OG 2P 2O2
      add angle 1OG 2P 2O3
      add dihedral   1CA 1CB 1OG 2P
      add dihedral   1CB 1OG 2P  2O1
      add dihedral   1CB 1OG 2P  2O2
      add dihedral   1CB 1OG 2P  2O3

patch dep
   reference=1=( resid 125 ) reference=2=( resid 401 )
If the patches were done correctly, the .mtf file should show a bond
between these 2 atoms.

Now, the .par file (the ligand parameter file) must be
editted to include the bond length of the newly formed bond.
Additionally, any new angles and dihedrals must also be added
to the .par file.  If any of these parameters are missing,
the minimization/annealing will crash, and the end of the log file will
indicate the bond lengths, bond angles, or dihedrals that
are still required.

If you have any other questions, send an e-mail to me and I will try to help with any problems.

Don Ronning
Graduate Student
Texas A&M University
Office #: (979) 862-7639