Appendix B Parameter Files and Their Origins

There are number of parameter files available. Immutable versions are stored in the directory, CGDATA. The file names used for 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.

There are four types of parameter files available; protein, DNA, AMBER, and obsolete. The protein parameter files are called PARAMn. The DNA parameter files are called PARMDNAn. The AMBER parameters files begin with AMBER, and the obsolete files are the other files which begin with PARM.

This appendix begins with an essay by David J. States describing the development of the PARAMn. The remainder of the appendix lists the titles from all the parameter files.

All the parameter files except for the AMBER files were either in CHARMM version 16 or were derived from them.

Parameters for any amino acid topology files

• PARAM1: Development of the PARAM series of parameter files.
• PARAM2: Has stuff for CO to Heme.
• PARAM3
• PARAM4
• PARAM5

Parameters for proteins and Nucleic acids together

• AMBERPARM: AMBER v.3 parameter set.
• AMBER94PARM: AMBER v.4 parameter set (1994).

Obsolete Parameters for proteins

• PARMEXEL
• PARMFIX10
• PARMFIX9
• PARMFIX8
• PARMFIX7
• PARMFIX5
• PARMFIX2
• PARMALLH

Parameters for DNA.

• PARMDNA4
• PARMDNA3
• PARMDNA1