This appendix contains a description of the various topology files available for CONGEN users. For CONGEN version 2 and beyond, we anticipate providing only one topology file in binary form, but all older and obsolete files will be provided in source form, although they may not be readable without some editing. All topology files are stored in CGDATA. The file names used consists of an alphabetic part followed by a number, e.g. RTOPH. There are two copies of each file; one with extension, .INP, which is a character files used as an command file to generate the binary file, with extension, .MOD. The .INP is meant for human eyes; the .MOD files are meant for CONGEN to read. The numeric part of each name is its version number. In general, one should use the highest version number of a file.
Five types of residue topology files are currently available. Three contain the twenty amino acids, but with different representations. RTOPn holds extended atom topologies; RTOPHn holds explicit hydrogen residue topologies; and RTOPALLHn holds all hydrogen residue topologies. The fourth topology file type, RTOPDNAn, is for DNA residues and the phosphates connecting them. These DNA files have not been used very much, so results obtained using them must be treated with especial care. Also, the DNA and protein files cannot be used together because of differences in the selection of atom type codes.
The fifth type of topology file is the AMBER topology file based on the AMBER potential1. At the present time, only the united atom topology file is available.
The remainder of this section lists the comments in the topology file themselves, along with some further explanations of the rationale behind particular versions.
All the topology file except for the AMBER files were either in CHARMM version 16 or were derived from them.
Extended atom topology files
Explicit hydrogen topology files
All hydrogen topology files
DNA topology files
AMBER topology files
 Scott J. Weiner, Peter A. Kollman, Dzung T. Nguyen and David A. Case, "An All Atom Force Field for Simulations of Proteins and Nucleic Acids", J. Comput. Chem 7, 230-252 (1986)