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The sidechain topology file describes how sidechain atoms are to be constructed. It is assumed that backbone atoms N, CA, and CB have been constructed prior to sidechain construction. The construction of sidechain is broken into clumps of atoms, where a single free torsion angle determines all the atoms in the clump.
The sidechain topology file may be used for limited conformational searches of any molecule. As long as one has a core of atoms whose positions are either known or easily constructable, one can define a description of how to construct the remaining atoms while sampling over all the rotatable torsion angles.
The sidechain topology file is a free format file containing a series of commands which fill the sidechain topology data structure used by CONGEN command. This data structure consists of a set of residues where each residue is made up of a set of free torsions (called clumps). Each clump has a rotational symmetry number associated with it as well as an option identifier for the clump. The identifier is useful when one is searching over a subset of clumps.
The clumps consist of a set of atom specifications. Each atom specification has the IUPAC names of four atoms arranged to form a constructor as used in the internal coordinates (see Internal Coordinates), and the bond length, bond angle, and torsion angle used in that constructor.
There are two sidechain topology files available,
CGDATA:TOPCGEN3.INP, for explicit hydrogen topology files, and
CGDATA:TOPALLHCG.INP, for all hydrogen topology files. The
subroutine, STREAD, is used to read this file.
The commands read in the sidechain topology file follow closely to the data structure. The commands are as follows:
RESIdue res [SPECIAL]
The residue command specifies the start of a new residue specification. The residue name given is matched against the residue names in the PSF (see Data Structures), when a sidechain degree of freedom is processed. The SPECIAL option is used to signify a sidechain that requires special processing, but presently, it is not used by the program. A RESIDUE command must be specified before any clumps.
CLUMP int [NAME word]
The CLUMP command specifies the start of a new clump within a residue. A clump command must precede any atom specifications.
The integer operand specifies the rotational symmetry of the clump. E.g., a symmetry of 1 means the full 360 degree range of the torsion must be sampled; a symmetry of 3 means only 120 degrees must be sampled. The optional name is used to identify the clump. In the absence of a specification, the name is taken to be the number of the clump within the residue.
{ FREE }
ATOM iupac iupac iupac iupac real real { real }
{ ADD real }
The ATOM command specifies how a particular atom is constructed. The first four operands give the IUPAC name for the atom. Prefixes may be used with this IUPAC names, and they are interpreted in the same way as residue topology file names are, see Linkage Atom Naming. An IUPAC name of N is processed specially, to wit, if it is not found within the residue, then NT is searched for.
The next two operands specify the bond length in Angstroms and the bond angle in degrees. If specified as 0, then CONGEN will search the parameter file (see Data Structures), for the equilibrium values. In the files provided with CONGEN, the rings (i.e. His, Phe, Trp and Tyr) have the bond lengths and angles explicitly specified; their values are determined using energy minimization with constraints to ensure planarity and symmetry. (The CONGEN parameters for bond lengths and angles are not perfectly consistent for these rings, which result in small deviations from symmetry and higher energies.)
The torsion angle is specified in the final parameter as either FREE, meaning that it is the degree of freedom for the clump; ADD real, when the real number is added to the value of the degree of freedom (the FREE value); or just a number which is used directly as the torsion angle. All angles are in degrees.
The order of atom constructors is important in that the first three atoms in any constructor must be present when the fourth atom is built. Thus, the order must reflect construction from the backbone out.
PRINT { ON }
{ OFF }
This command controls whether the topology file commands are printed as they are read. The default is no print.
COPY { res } [INVERT]
This command will copy the information about one residue into the description of a second residue. The INVERT option will cause all the torsion angles specified in the non-free atom constructor to be negated. This results in an inversion of chirality for the residue, and is currently used for constructing D amino acids. The COPY command is useful when two residues have either similar or identical sidechains, and one wishes to avoid the problems with duplicating data that should be the same. The effect of the COPY command is the same as if the commands for the copied residue were inserted when the COPY command is specified.
END
This command terminates processing of sidechain topology commands.