Receptor - Advanced Settings Dialog Box

Receptor - Advanced Settings Dialog Box Features

• Per-atom van der Waals radius and charge scaling section
• Count aromatic H and halogen H-bonds section
  • Include aromatic H as donors option
  • Include halogens as options

Per-Atom Van der Waals Radius and Charge Scaling Section

As a more flexible method of softening the receptor potential, you can specify van der Waals radii and charges on a per-atom basis. If you specify per-atom scaling, the global scaling of nonpolar atoms is only performed on those atoms for which per-atom scaling factors are not specified.

Select one of the following options for scaling:

None

Do not do any per-atom scaling.

Read from input structure file

Read the radius and charge scaling factors from the input file for the receptor. This file must be in Maestro format, and must have the properties VdW radius scale factor (r_glide_atom_vdwscale) and Charge scale factor (r_glide_atom_coulscale) defined. These properties must have a value for each atom in the receptor. They are defined if you have previously set per-atom scaling factors.

Specify for selected atoms

Specify the scaling factors for selected atoms. You can make multiple selections and apply scaling factors to each. The selections should be mutually exclusive.

van der Waals radius scale factor text box

Specify the van der Waals radius scaling factor for the selected atoms. This value will be applied to the atoms that you pick.

Charge scale factor text box

Specify the charge scaling factor for the selected atoms. This value will be applied to the atoms that you pick.

Select atoms for scaling factor picking tools

Use these picking tools to select a set of atoms. The option menu offers the choice of Residues, Chains, Molecules, or Entries. For other types of atom selections, you can use the Select button. When you have made the selection, a row is added to the table with the ASL expression for the selected atoms and the current values of the scaling factors.

Table

Lists the selections made and the scaling factors for each selection. A row is added to the table after each selection.

Delete and Delete All buttons

Delete the selected table rows, or delete all rows.

Count aromatic H and halogen H-bonds Section

These settings control whether aromatic hydrogens are considered to form hydrogen bonds, whether halogens can form hydrogen bonds as an acceptor or weak bonds with electronegative atoms (like oxygen) as a donor. These bonds are treated like other hydrogen bonds: they are included in the rough scoring in grid generation, in the scoring function, and are considered for hydrogen-bond constraints.

Include aromatic H as donors option

Select this option to include aromatic ligand hydrogen atoms as donors during docking.

Include halogens as options

Select this option to include nonbonded interactions with ligand halogens. You can choose one of two possibilities for halogen interactions:

• acceptors—Treat halogens as acceptors of hydrogen bonds.

• donors—Treat halogens as donors of nonbonded interactions with electronegative atoms, such as oxygen. This effect originates in the positive potential on the halogen in line with the bond axis (sigma hole).