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Ligand Docking — Ligands Tab |
Use the Ligands tab of the Ligand Docking panel to specify the source of ligands to be docked or scored, set size limits for skipping ligands, and optionally to change the settings for van der Waals radii scaling of nonpolar ligand atoms.
There are two sections in this tab:
Use this section to specify the source of ligands to be docked (or scored in place), the partial charges to use, and to set size thresholds for skipping ligands.
For accurate docking, the ligands you specify must satisfy these four conditions:
.mae.gz or .maegz) or
SD file (.sdf.gz or .sdfgz).
Ligand preparation, for example using LigPrep, is strongly recommended before Glide ligand docking.
Glide automatically skips ligands containing unparametrized elements, e.g., tin, or atom types not supported by the OPLS force fields, such as explicit lone pair "atoms".
The Ligands to be docked section includes the following sets of options:
Choose the source of the ligands from this option menu, from the following options:
Workspace (included entries)—Dock the structures in the Workspace. If you select this option, the entries in the Workspace must all be valid ligands, as described above. You must ensure that the structures in the Workspace satisfy the requirements.
Project Table (selected entries)—Dock ligands that are selected entries in the Project Table. For more information about the Project Table and entry selection, see the Project Table Panel topic.
Files—Dock ligands from one or more files. Enter the file names in the File name text box, or click the Browse button to navigate to and select the ligand files. The files can be in any of the supported formats, and you can have files of different format in a single job. By defaut, all structures in each file are docked.
If you select a single file, you can specify a particular range of ligands to
dock, using the Range controls:
To start at a ligand other than the first, edit the value in the first text
box.
To end at a value other than the last, deselect End and
edit the value in the second text box.
If a Glide job run with a single ligand file terminates abnormally, you can set the initial ligand number to pick up after the point in the input ligand file at which the problem occurred.
Select this option to use partial charges from the input structures instead of those from the force field. This option enables you to use improved partial charges, for example from a Jaguar or a QM-Polarized Ligand Docking calculation.
This text box sets the maximum number of atoms a ligand structure may have if it is to be docked. Ligand structures in the input file that have more than the specified number of atoms will be skipped. The default (and maximum) is 500 atoms. You can reduce the maximum number of atoms a, if the active-site region is small and enclosed, to speed up a docking calculation on a large ligand database.
This text box sets the maximum number of rotatable bonds a ligand structure may have if it is to be docked flexibly. Ligand structures in the input file that have more than this number of rotatable bonds are skipped. The default (and maximum) number is 100 rotatable bonds. If only relatively small or rigid ligand "hits" are wanted, you can decrease the value of r. If you use torsional constraints, the rotatable bonds that are constrained are excluded from the number of rotatable bonds. The text box is not available if you have selected Refine or Score in place in the Settings tab.
Glide does not allow for flexible receptor docking. (For information about Glide/Prime Induced Fit docking, see the document Induced Fit Docking). However, successful docking sometimes requires that the ligand or the receptor "give" a bit in order to bind. To model this behavior, Glide can scale the van der Waals radii of nonpolar atoms (where nonpolar is defined by a partial charge threshold you can set), thereby decreasing penalties for close contacts. By default, scaling is performed for qualifying atoms in the ligand, but not those in the receptor. Ligand atom radii scaling settings can be changed using the options in this section.
To scale receptor atom radii, you must choose the appropriate options in the Receptor Tab of the Receptor Grid Generation panel prior to grid generation.
The Scaling factor text box specifies the scaling factor. The default is 0.80. To turn van der Waals radii scaling off, set the scaling factor to 1.0. Full penalties for close contacts of nonpolar ligand atoms will then be used.
Scaling of vdW radii is performed only on nonpolar atoms, defined as those for which the absolute value of the partial atomic charge is less than or equal to the number in the text box. Since this is an absolute value, the number entered must be positive. The default for ligand atoms is 0.15.
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