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3.1.5 The Format of a Residue Topology File

Here is a description of what is in residue topology files (as they are stored in text files). You may use this format if you specify the CARD option in the READ command. The format of binary files depends on the current implementation of the RTF data structure. See the file RTF.FCM in the CONGEN source directory for more details. These files are read by RTFRDR, a subroutine in RTFIO which should be be consulted for formats and the final word on what is actually done with these files.

The purpose of residue topology files is to store the information for generating a representation of macromolecule from its sequence. For each residue, CONGEN requires a description of all bonds, bond angles, dihedral angles, improper torsion angles, partial charges, chemical types, and hydrogen bond donors and acceptors. By linking residues in the sequence together, segments in the molecule are constructed.

The linkage between successive residues is determined when the segments are generated (see Generate Command). It is specified in the residue by using special prefixes on the atom names which refer to residues either ahead of or behind the current residue. In the case of cyclic segments, the program will wrap references around the cycle.

The residue topology files begin with rtop. There are two forms, binary module (.mod) and card format (usually .inp). The card format files are used only for creating binary modules and therefore are structured as input files for CONGEN, beginning with a run title and the command READ RTF CARD, followed by the actual topology file.

The first section of the topology files is a title section in the usual format of up to ten lines delimited by a line containing only a `*' in column 1.

The next line is a set of up to 20 numbers of which the first number gives the topology file format version number. This number be set to 200 for CONGEN to read the remaining file correcting in free field format. If some other number is present or the number is missing, the program will attempt to read the topology file in the current format.

The remaining information is read in free field format as commands to define the RTF. The ordering of the commands is important in that some information is needed to define others (i.e. the atoms of a residue should be defined before the bonds between them). The recommended structure of this file is: 

     Initial setup:
             TYPE declaration
             MASS specification for each atom type (also hydrogen
                  bond donor and acceptor classifications)
             DECLarations of out of residue definitions
             ORDEr specification for atom order.
             SET  command for charge patching
     For each residue:
             RESIdue name and total charge specification
             ATTRibute option to specify
             ATOM definitions within this residue
             BOND specifications
             ANGLe specifications
             DIHEdral angle specifications
             IMPRoper dihedral angle specifications
             DONOr specifications
             ACCEptor specifications
             BUILD information
             GROUPing definitions
             GENErate options
             COPY option to copy information from other residues
     Closing:
             END statement
     Display control:
             PRINT option

The format above is not rigid.

There exists the facility to automatically generate the bond angles, torsion angles, hydrogen bond donors and acceptors, and the BUILD information. It is also possible to delete terms that are generated automatically, and therefore, it is possible to correct any deficiencies in the automatic schemes.