The “parameter_file” command allows you to specify a new parameter library file that contains the various force field parameters.  In most cases, you will not need to modify these values, but you can make changes if you have special needs for your application.

The standard AutoDock 4 parameters are in the file “AD4_parameters.dat” which can be found in the “autodocksuite-4.n.m/src/autodock-4.x.y” directory of the AutoDock 4 distribution, where n and m are the major and minor version numbers of the AutoDock Suite, and x and y are the major and minor version numbers of AutoDock. These are the default values that are “baked in” to AutoGrid 4 and AutoDock 4, and are the values that will be used if you do not specify your own parameter file explicitly in your GPF or DPF with the “parameter_file” command.

You can add new atom types and parameters to this file, or modify the existing ones.  Please refer to the AutoDock4.2.6_UserGuide for information on the parameters and format of the file. If you come up with new or modified parameters, we would like to know about them, so we can incorporate them in future releases.  Thanks!