GOLD has a front end written in Tcl/Tk that allows configuration files to be generated and edited. The program can also be run directly from this graphical interface.
Getting started describes how you can run GOLD using the front end.
The front end is a form interface, which allows the user to set the values of GOLD parameters by typing values into entry boxes. Functionality is provided through buttons in the top panel.
On-line, context-dependent help is available in the front end, by clicking the
middle mouse button on the item for which information is required. For example, clicking on 
, brings up this
help dialog window:
Each of the main panels in the front end is now described.
 | This button runs GOLD through the graphical interface after saving the configuration. |
 | The Default button brings up a menu of GOLD defaults. The standard default values have been shown to be robust over a large number of test systems. For more details about other default settings that allow GOLD to run faster see here. |
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 | This button saves the information that has been input to the front end as a "configuration file". Thus, the user can specify all the details of a calculation, save them in the configuration file, and then exit the front end. GOLD can then be run from the command line. |
 | Saves the configuration (i.e. the calculation details that have been input by the user), submits the GOLD calculation as a background job, and then exits the front end. |
 | Terminates the front end. |
 | The configuration file entry. This holds the name of the configuration file. When you hit the Save&Exit button, the current configuration is saved to this file name (typically called gold.conf). To load a previously created configuration file into the front end, enter the file name into this box and hit return. To pick a previous configuration file, click on the button. You can edit configuration files by loading them into the interface, editing them, and then saving them (possibly to a new name). |
 | Brings up these pages. |
Input Parameters and Files
 | Click on the button to pick a ligand and specify the number of times it should be docked (the ligand count in the "No Ligands" entry box will then be incremented: see the getting started guide). |
 | Click on the button to pick the protein data file (the filename will then appear in the entry box: see the getting started guide). |
 | Click on the button to select an output directory (the directory name will then appear in the entry box). Alternatively, type a new directory into the entry box. All output files will be written to the specified directory, which will be created if it does not already exist. |
 | If the ligand input file is in SYBYL MOL2 format, then click on the check button if you want GOLD to set atom types automatically. (Automatic atom typing will always be performed if the input file is in any other format.) |
 | If the protein input file is in SYBYL MOL2 format, then click on the check button if you want GOLD to set atom types automatically. All residues must be complete. (Automatic atom typing will always be performed if the input file is in any other format.) |
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Click on this button to allow early termination. This means that the program will stop if the early termination condition (see directly below in this document) is satisfied. |
 | Use these boxes to specify an early termination condition. Here, for example, GOLD will terminate ligand docking if the top 3 solutions are within 1.5 Angstrom RMSD of each other (the RMSD calculation takes account of symmetry). |
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These radio buttons allow the specification of the centre and extent of the binding site. See the getting started guide for more information. |
 | The radius of the binding site. This should be large enough to include all residues that might reasonably interact with the ligand. |
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Click this button to use the cavity detection algorithm. |
 | Set this check button if the ligand is covalently bound. See the section on covalent binding. |
 | You can click on this button to make the grommitt viewer display show the current top solution in the protein. You should set this to "nothing" if GOLD is to be run in the background. |
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Click on this button to edit the parameter file. If the parameter file is set to "DEFAULT" then the standard GOLD distribution parameter file is copied to the current directory. |
 | The entry box should say "DEFAULT" if you want to use the default GOLD parameter file. You can click on the button to pick an alternative parameter file, or alteratively type a filename into the entry box. See the parameter file page for more information. |
Fitness Function Settings
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Hit this button to get a menu for fitness function flags: |
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 | Click to add/edit constraints. |
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Normally, a bump check is made to guard against unreasonably close contacts between ligand and protein atoms. However, you can permit n ligand atoms to penetrate the protein by entering n in the entry box. |
 | Set the check button to use torsional distributions extracted from the Cambridge Structural Database. The torsional distributions are used to restrict the ligand conformational space sampled by GOLD. See the page on torsional distributions. |
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Click on this button to edit the GOLD torsional distribution file. If you are using the default torsional distribution file, it will be copied to the current directory. (You may use the EDITOR environment variable to specify the editor you require; by default, jot is used.) |
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Click on the Tordist File button to pick a torsional distribution file. Alternatively, type the file into the entry box. The entry "DEFAULT" uses the default torsional distribution file in the GOLD distribution directory. See the torsional distribution file page for more information. |
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The parameters start_vdw_linear_cutoff and initial_virtual_pt_match_max can be altered to make GOLD run faster. As a GOLD calculation progresses, certain parameters within the fitness function are annealed. This annealing process allows poor hydrogen bonds and some initial bad bumps to occur at the beginning of a GA run, in the expectation that they will evolve to better solutions. However, the annealing must be gradual and the population allowed plenty of time to adapt to changes in the fitness function. |
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The easiest way to make GOLD run faster is to reduce maxops and n_islands. However, this should be done with appropriate changes to the variables start_vdw_linear_cutoff and initial_virtual_pt_match_max. See here for more information. |
Genetic Algorithm Parameters
See the page on GOLD parameters for an explanation of the genetic algorithm parameters.
 | Set the GA population size in the entry box. |
 | Set the GA selection pressure in the entry box |
 | Set the maximum no of GA operations in the entry box. |
 | Set the number of GA islands used in the entry box. |
 | Set the GA niche size in the entry box. Set to zero to turn off niching. |
 | Enter the operator weight for migration in the entry box. |
 | Enter the operator weight for mutation in the entry box. |
 | Enter the operator weight for point crossover in the entry box. |
After hitting the run button, output from GOLD is displayed in a separate window. You can use the Interrupt GA button to interrupt GOLD and terminate the docking run.
 | Use this button to rank solutions that have been already been produced by GOLD. |
If any error conditions are encountered, they will be displayed in another window.
