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ADT |  |
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Introduction | |
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Ligand | |
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Grid | |
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Docking | |
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Run | |
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Analyze | |
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ADT | |
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Introduction | |
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Ligand | |
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Grid | |
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Docking | |
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Run | |
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Analyze | |
Set Macromolecule
Choose Macromolecule
If the macromolecule is already present in the Viewer, 'Choose Macromolecule' allows the user to select it via a MoleculeChooser.
Select Macromolecule Filename
'Select Macromolecule Filename' starts a file browser for selecting the macromolecule filename. The macromolecule must be in pdbqs format. NB: the chosen macromolecule is NOT read into the viewer by this route.
If the small molecule is already present in the Viewer, use this option to pick it.
'Read Autotors-Formatted Ligand File' lets the user pick a filename. This file must contain the results of Autotors: i.e. key words such as ROOT and ENDROOT are correctly placed , torsion activity has been set and the number of torsional degrees of freedom is included on the last line.
Ligand Parameters which can be set by the user include:- whether or not to use a floating point grid map
- how to set the initial state of the ligand's position and relative dihedral offset
- what coefficient of torsional degrees of freedom to use
- whether to specify initial dihedrals
- The GUI containing the Ligand Parameter Options opens when a new ligand is selected. It may be re-opened at any time with 'Adjust Ligand parameters'.
Set Search Parameters
The following figures show the menus and dialog boxes used to set up various types of dockings.
Simulated Annealing Parameters
Genetic Algorithm Parameters
Local Search Parameters
Set Docking Run Parameters
Write DPF
Write the docking parameter file for the chosen algorithm.
Edit DPF
allows the user to view and make changes to the docking parameter file.
Get values from a DPF
Re-reading a pre-existing docking parameter file, using `Get values from a DPF', allows the user to re-use selections made previously.
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ADT | |
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Introduction | |
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Ligand | |
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Grid | |
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Docking | |
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Run | |
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Analyze |