2.5 Data Structures

There are a number of data structures that CONGEN manipulates. Many of these data structures are important for most operations; others which are less important, are described with the commands that use them. Much more specific information is available in the various common blocks whose extension is .FCM in the source directories.

The important data structures are given below: Each data structure name is followed by its abbreviation which is used as its name in commands.

1. Residue Topology File (RTF). The residue topology file stores the definitions of all residues. The atoms, atomic properties, bonds, bond angles, torsion angles, improper torsion angles, hydrogen bond donors and acceptors and antecedents, and non-bonded exclusions are all specified on a per residue basis. The RTF also specifies the list of chemical type which are used in the parameter file. This file is required for any calculations.

2. The Parameters (PARA or PARM). The parameters specify the force constants, equilibrium geometries, Van der Waals radii, and other such data needed for calculating the energy. The list of atom type codes comes from the RTF. The parameters are required for any calculation, and they depend on the list of chemical types provided in the RTF. The parameters must be consistent with the topology file in that they must designed together. In addition, there must be one and only one non-bonded parameter for each atom type specified in the topology file.

3. Protein Structure File (PSF). The protein structure file is the concatenation of information in the RTF. It specifies the information for the entire structure. It has a hierarchical organization wherein atoms are grouped into residues which are grouped into segments which comprise the structure. Each atom is uniquely identified within a residue by its IUPAC name; each residue is uniquely identified in the segment by a residue identifier which is the character form of the residue's position in the segment; and each segment is identified by a segment identifier specified by the user. This information is required for any calculations.

4. The Coordinates (COOR). The coordinates are the Cartesian coordinates for all the atoms in the PSF. There are two sets of coordinates provided. The main set is the default used for all operations involving the positions of the atoms. A comparison set (also called the reference set) is provided for a variety of purposes, such as a reference for rotation or operations which involve differences between coordinates for a particular molecule.

5. The Non-bonded List (NBON). The non-bonded list contains the list of non-bonded interactions to be used in calculating the energies as well as optional information about the charge, dipole moment, and quadrupole moments of the residues. This data structure depends on the coordinates for its construction and must be periodically updated if the coordinates are being modified.

6. The Hydrogen Bond List (HBON). The hydrogen bond list contains the list of hydrogen bonds. Like the non-bonded list, this data structure depends on the coordinates and must be periodically updated.

7. The Constraints (CONS). The constraints are harmonic potentials placed on selected atomic positions or on dihedral angles. The purpose of these constraints is to limit motion of those atoms or torsions or to force the molecule to assume a particular conformation. Normally, there are no constraints on the molecule. One should note that this data structure does not hold either constraints related to SHAKE or motion constraints where atoms are prevented from moving entirely.

8. The Internal Coordinates (IC). The internal coordinates data structure contains information concerning the relative positions of atoms within a structure. This data structure is most commonly used to build or modify cartesian coordinates from known or desired internal coordinate values. It is also used in conjunction with the analysis of normal modes. Since there are complete editing facilities, it can be used as a simple but powerful method of examining or analyzing structures.

9. The Images data structure (IMAGES). The images data structure determines and defines the relative positions and orientations of any symmetric image of the primary molecule(s). The purpose of this data structure is to allow the simulation of crystal symmetry or the use of periodic boundary conditions. Also contained in this data structure is information concerning all nonbonded, H-bonds, and ST2 interactions between primary and image atoms.