Author: Sam DeLuca

An overview of params files

Params files store a variety of chemical and geometric information.

A set of params files for commonly seen residues and metals is included with rosetta, and can be found in rosetta_database/chemical/residue_type_sets

The following lines are typically found in Ligand params files. This does not represent a complete documentation of the params fileformat. These files are read in core/chemical/residue_io.cc

• NAME The 3 letter name of the Residue. Must be unique among all residues loaded into Rosetta

• IO_STRING The 3 letter and 1 letter codes representing the residue. 3 letter code is the same as NAME, 1 letter code is Z by default.

• TYPE The type of residue being represented, should be 'LIGAND' for ligands, or 'POLYMER' for protein or DNA residues

• AA The amino acid type. Should be "UNK" for ligands

• ATOM The PDB atom name, Rosetta AtomType, MM AtomType, and charge. an atom line looks like this:

  ATOM  C17 CH1   X   0.13
  

  Where C17 is the PDB atom name, CH1 is the Rosetta AtomType, X is the MM AtomType, and 0.13 is the charge. The PDB atom names must be unique within each params file.

• BOND Defines a bond connection, two PDB atom names are specified

• CHI Defines a rotatable chi angle. A chi angle number is specified, followed by the names of the four atoms defining the angle

• PROPERTIES A series of properties describing this ligand type or residue type. Allowed properties include (though this list is not exhaustive): PROTEIN POLYMER LIGAND COARSE METAL METALBINDING DNA RNA CARBOHYDRATE SURFACE POLAR CHARGED AROMATIC TERMINUS LOWER_TERMINUS UPPER_TERMINUS SC_ORBITALS.

• METAL_BINDING_ATOMS A list of the names of atoms in this residue/ligand that can form covalent bonds to metal ions.

• NBR_ATOM The PDB name of the "neighbor atom". In the case of ligands, this defaults to the atom that is closest to the geometric center of the ligand

• NBR_RADIUS The radius of gyration of the ligand, used to define the overall size of the ligand.

• ICOOR_INTERNAL The internal coordinates of an atom. The format goes backwards and looks like this:

  ICOOR_INTERNAL    A4  179.932453   59.543328    1.238233   A3   A2   A1
  

  And the fields are the following:

  • Child atom
  • phi angle (torsion angle between A1, A2, A3, A4)
  • theta angle (improper angle = (180 - (angle between A4, A3, A2)))
  • distance (between A4 and A3)
  • parent atom
  • angle atom
  • torsion atom

• PDB_ROTAMERS The path to a PDB file containing ligand rotamers

See this page for more information: http://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Workshops_Appendix_B.pdf