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AutoDock 4 makes it easier to change the weights for the various terms in its scoring function than in AutoDock 3. This is done using AutoDock 4 parameter files, and these can be specified in the GPF and DPF using the "parameter_library" keyword ("parameter_file" also works). The "parameter_library" keyword requires one argument, the name of the parameter file. Note that if the "parameter_library" keyword is not specified, AutoGrid 4 and AutoDock 4 will use default values that are compiled into the executable. In AutoDock 4.0 these defaults are the same as in "AD4_parameters.dat".

AD4.1_bound.dat by morris — last modified 2009-05-29 09:42
This is the default parameter file for AutoGrid 4.2 and AutoDock 4.2; the coefficients of this model were derived using the assumption that the unbound ligand has the same conformation as the bound ligand. Please note these two caveats: 1- If the DPF keyword "compute_unbound_extended" is present in the docking parameter file, AutoDock 4.2 will switch from this set of parameters to those in AD4_parameters.dat. 2- If you intend to use the parameters in AD4_parameter.dat, the same parameters should also be used for the AutoGrid 4.2 calculation.
AD4.1_compact.dat by morris — last modified 2009-05-29 08:56
The coefficients of this model were derived using the assumption that the unbound ligand is in the compact conformation. This is not currently supported in AutoDock 4.
AD4.1_extended.dat by morris — last modified 2009-05-29 09:43
This is the default parameter file for AutoGrid 4.0.0 and AutoDock 4.0.1. It can also be used as an alternative parameter file for AutoGrid 4.2 and AutoDock 4.2, although the AD4.1_bound.dat file is the default for version 4.2. The coefficients of the model were derived using the assumption that the unbound ligand is in the extended conformation. The DPF keyword "compute_unbound_extended" _must_ be used with this set of parameters.
AD4_parameters.dat by morris — last modified 2008-03-12 13:11
This is the default parameter file for AutoGrid 4.0.0 and AutoDock 4.0.1; the coefficients of the model were derived using the assumption that the unbound ligand is in the extended conformation. The DPF keyword "compute_unbound_extended" must be used with this set of parameters.

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