Ligand-Based Advanced Options Dialog Box

Ligand-Based Advanced Options Dialog Box Features

• General options
• Use linkers section
• Use WaterMap section
• Filtering options

General options

Set general output options:

• Log file verbosity—Specify the amount of output to write to the log file.
• Allow structures containing Glide linker grownames—Allow the use of protocores with linkers that were generated by receptor-based core hopping, which involves Glide docking. The linker labeling in these protocores is ignored if you select this option, otherwise their existence is considered an error, and the job fails.

Use linkers section

Select Use linkers to allow the addition of linkers to the attachment points of the candidate cores. The linkers are read from a file of linkers. A standard file, stored in the distribution, is used for this release. The file selection controls can be ignored.

Use WaterMap section

Select Use WaterMap if you want to score ligands with information contained in a WaterMap file. Click Browse to navigate to the file, or enter the file name in the text box.

Filtering options

The filtering options set criteria for hydrogen bonds to the receptor, if present, or for matching donor or acceptor atoms in the template.

• Maximum side-chain RMSD— maximum permissible root-mean-square interatomic deviation of the newly placed side chains from their original positions on the template.

• Receptor H-bond cutoff—maximum length of a hydrogen bond to the receptor, if present.

• Template acceptor/donor atom cutoff—Maximum distance from a designated template acceptor or donor atom for a corresponding protocore acceptor or donor atom to be considered a match, when requiring acceptor/donor matches.