1. Missing parameters are listed by parm.
2. Go through them and add them to a file mol.dat
   The new files should be collected in /temp4/bio/Data/Amber (look there first)
   
3. They are either taken from similar amino-acid residues in $AMBERHOME/dat/parm96.dat (less accurate), or
calculated from the a quantum chemical hessian by /temp4/bio/Bin/describe (better).
 

1. Optimise the metal site at the TPSS/def2-SV(P) level (or similar; template). A typical model is Zn(SCH3)2(imidazole)2.
   
   
2. Run a frequency calculation. From the Hessian, force constants of all relevant bond, angles, and dihedrals can be extracted. This is done automatically by /temp4/bio/Bin/describe from G94/G98 output or Turbomole control+hessian  file. The program is based on the algorithm suggested by JM Seminario in Intern. J. Quant. Chem., Quant. Chem. Symp. 30 (1996) 59-65). For the dihedrals, you have to decide the periodicity from the structure and other considerations.
   
   You should first construct a file with atom types with the following format (template):
   title lines ended by a blank line
   
   Residue name (three letters)
   atom_name atom_type (natom lines; each four letters; free format, separated by blanks)
   
   Run the program describe and answer the questions. If you do not know what to do, try the default.
   
   
3. Run a Merz-Kollman calculations of ESP charges with a higher-than-default density of ESP points, cf. the RESP page.

Template of the atmtyp file

Template Gaussian input file

The default_bonds file