Making topology files

The topology statement consists of information about "residues" that combine to form a particular macromolecule. The data include descriptions of atoms, assignments of covalent bonds (connectivity), bond angles, and other information. The information provided by the topology statement is used by the segment statement and the patch statement to generate the molecular structure.

CNS, like many other macromolecular mechanics/dynamics packages, can use a classification scheme that employs chemical atom types. This system of atom classification makes force fields transferable between groups that are almost equivalent and thereby allows one definition to work for all or almost all instances of that type of atom. The specific atom classifications can be arbitrarily defined by the user. The parameters of chemical atom types are given in the parameter statement. Electric charges are specified on an individual atom basis, since they are less transferable than stereochemical parameters. For historical reasons, atomic masses may also be specified on an individual atom basis, but there exists the mass statement outside the residue statement that assigns default atomic masses on a basis of chemical atom type. Apart from the type-based parameter retrieval, CNS also provides atom-based parameter statements, which allow one to specify any parameter on a per-atom basis.

The topology statement is invoked from the main level of CNS (the topology information is most often read from a library file.

  topology 
    { topology-statements }
  end

  @CNS_TOPPAR:protein.top

The CNS topology statements are as follows:

• AUTOgenerate ANGLe=logical DIHEdral=logical END works only on regular residues, not on patch residues. It automatically generates all possible bond angles based on the connectivity list of the particular residue. It operates on the residues following the statement until the next autogenerate statement appears.
• MASS=type=real adds a default mass assignment for the specified type of atom to the topology database. The real number is defined in atomic mass units. This value will be used by default for all atoms of that type unless an explicit MASS statement is given in the atom statement (see below).
• RESEt erases all previous entries into the topology database.
• RESIdue residue-name { residue-statements } END adds a residue to the topology database.
• PRESidue residue-name { [ ADD | DELEte | MODIfy ] residue-statement } END adds a patch residue to the topology database.

The allowed residue statements are as follows:

• ANGLe atom atom atom adds a bond angle made by the three atoms to the residue database. It should not be used if autogenerate angles are active.
• ATOM [patch-character] atom atom-statement END adds an atom to the residue database. The statement defines atom as a four-character string specifying the name, and atom statement specifies atom type, charge, and mass. The patch character is a 1-character string and may be used only for PRESidue.
• BOND atom atom adds a covalent bond between the specified atoms to the residue database. The atoms have to be defined previously by atom statements.
• DIHEdral atom atom atom atom [MULTiple integer] adds a dihedral angle to the residue database. The dihedral angle (ijkl) is defined by the angle between the plane made by the atoms (ijk) and the plane made by the atoms (jkl). The dihedral statement should not be used if autogenerate dihedrals are active, unless multiple dihedral angles are wanted. MULTiple specifies m dihedral angle entries for the same instance of four atoms. This allows one to specify a cosine expansion for the dihedral angle potential energy. It must be accompanied by a corresponding DIHEdral angle parameter entry with appropriate multiplicity.
• GROUP partitions the atoms into nonbonded groups.
• IMPRoper atom atom atom atom [MULTiple integer] adds an improper angle to the residue database. The definition is identical to the DIHEdral angle, but it uses a different set of parameters. As in the case of the DIHEdral angle, the improper angle (ijkl) is defined by the angle between the plane made by the atoms (ijk) and the plane made by the atoms (jkl). MULTiple specifies m improper angle entries for the same instance of four atoms. This allows one to specify a cosine expansion for the improper angle potential energy. It must be accompanied by a corresponding IMPRoper angle parameter entry with appropriate multiplicity.

An atom is the defined by a character string (a maximum of 4 characters in length). The definition of an atom in a residue or patch residue can include the following statements:

• CHARge=real specifies an electrostatic charge in units of one electron charge. This affects the electrostatic energy.
• EXCLude=( { atom } ) specifies explicit nonbonded interaction exclusions. The atoms have to have been defined previously by an atom statement.
• MASS=real overwrites a default mass given by a mass statement outside the residue statement, in atomic mass units.
• TYPE=type specifies the chemical atom type, a string with up to four characters. The atom type is used to retrieve type-based parameters.

TOPOlogy 
   MASS   H      1.008 
   MASS   C     12.011 
   MASS   CH1E  13.019 
   MASS   CH2E  14.027 
   MASS   CH3E  15.035 
   MASS   N     14.0067 
   MASS   O     15.9994 

   AUTOgenerate ANGLes=TRUE END 

   RESIdue LEU 
     GROUp 
     ATOM N    TYPE=NH1   CHARge=-0.35   END 
     ATOM H    TYPE=H     CHARge= 0.25   END 
     ATOM CA   TYPE=CH1E  CHARge= 0.10   END 
     ATOM CB   TYPE=CH2E  CHARge= 0.00   END 
     ATOM CG   TYPE=CH1E  CHARge= 0.00   END 
     ATOM CD1  TYPE=CH3E  CHARge= 0.00   END 
     ATOM CD2  TYPE=CH3E  CHARge= 0.00   END 
     ATOM C    TYPE=C     CHARge= 0.55   END  
     ATOM O    TYPE=O     CHARge=-0.55   END  

     BOND N    CA 
     BOND CA   C 
     BOND C    O 
     BOND N    H 
     BOND CA   CB 
     BOND CB   CG 
     BOND CG   CD1 
     BOND CG   CD2 

     DIHEdral N    CA   CB   CG 
     DIHEdral CA   CB   CG   CD2  

     IMPRoper CA   N    C    CB  
     IMPRoper CG   CD2  CD1  CB  

   END 
END