2.7 Files Available for General Use

There are number of residue topology files, parameter files, coordinates files and files of other data structures available. The most important files generally available are residue topology and parameter files. Both such classes of files are stored for general use in the directory, CGDATA:. The file names used for both these files consists of an alphabetic part followed by a number, e.g. PARAM5. 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 is 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.

The current list of files which are in the best condition are as follows:

PARAM5

Parameters for all protein topology files.

RTOP8

Extended atom (no hydrogen) topology file. This topology has not been tested with conformational search.

RTOPH8

Explicit hydrogen (polar hydrogens only) topology file.

RTOPALLH7

All hydrogen topology file.

The DNA files are not usable with extensive review. The chemical type codes are not consistent with proteins, and the linkage scheme or the patching code has not been tested in years.

The directory, CGTD, contains a few protein coordinates assembled from a variety of sources.

For information on the general use of directories, and the files they contain, see Directory Names.

• Parameter Files: Origins of all the parameter files
• Residue Topology Files: Origins of the topology files (RTF)