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Ligand Docking — Output Tab |
The options in the Output tab control the final output of ligand poses that pass successfully through Glide's various scoring stages.
The features of this tab are options in a section called Structure output and an Advanced Settings button. Clicking the button opens the Ligand Docking - Output - Advanced Settings panel.
The final list of poses that pass Glide's criteria are written to a multi-structure pose file. The file is compressed by default. You can select one of two options for the file type:
This version of the pose file, which includes the receptor, is intended for use in the Project Table for viewing poses in the receptor binding site. For more information, see the topic Viewing Poses.
This option includes only the ligand structures in the output pose file. This version of the pose file cannot be used with the pose viewing facility, but may be appropriate if the output poses are intended for input to a subsequent Glide job, for example. The file can be written in Maestro or SD format; the choice is made from the option menu.
This option is not available if you chose to write XP descriptors or per-residue interactions, or if you have rotatable groups in the grid. These features require a pose viewer file.
Select this option to limit the total number of the predicted best-binding poses written to the sorted pose file. By default, all poses that pass the filters are reported. If you are docking a large number of ligands and want multiple poses per ligand, the pose file may take up a large amount of disk space.
This text box limits the number of poses per ligand written to the sorted pose file. The default choice of 1 pose per ligand is intended for database screening applications. A larger choice may be appropriate for lead-optimization studies or whenever several "reasonable" poses are wanted, for example, to generate a variety of docked poses for study with Liaison or another post-docking program.
This option allows you to perform a minimization of the poses following the final docking, and can be used for both flexible and rigid docking. The minimization optimizes bond lengths and angles as well as torsional angles, and rescores the poses using the scaled Coulomb-van der Waals term and the GlideScore. With this option there are two other controls:
Specify the number of poses per ligand to include in the minimization. This number must be greater than the number of poses per ligand that is written to the output file. The default is 5 for SP and HTVS, 10 for XP.
For XP docking, the pose is kept if the GlideScore is no higher than that of the original pose by less than the specified threshold, otherwise the original pose is kept. This text box is not available for SP and HTVS docking.
Apply strain correction terms when doing the final scoring. These terms are evaluated by optimizing each ligand pose as a free ligand, first with constraints on all torsions, then without these constraints. The difference is used to compute a penalty term for unreasonably high strain.
Write out per-residue interaction scores for a specified set of residues. The Coulomb, van der Waals, and hydrogen bonding scores, the sum of these three (Eint), and the minimum distances are calculated between the ligand and the specified residues. These values are written as structure-level properties for each ligand to the pose file, as well as to the log file. The residues can be specified by selecting one of these options:
For residues within N Å of grid center—Write scores for complete residues that have any atom within the specified distance of the grid center.
Pick residues to include—Pick the residues for which the scores are written. The residues are specified by clicking Specify Residue and using the picking controls in the dialog box that opens.
Write a report of the scores to the text file
jobname.rept for docking jobs and to
jobname.scor for score-in-place jobs. The report file
lists the poses in rank order by the selected final scoring function.
Compute the RMSD between the docked poses and the corresponding input
ligand geometries. The RMSD calculation is done in place with heavy atoms only.
The value is recorded as a Maestro property, named
Glide rmsd to input (internal name
r_i_glide_rmsd_to_input).
This button opens the Output - Advanced Settings dialog box, in which you can set options to screen out poses that either have too high an energy or are too similar to other poses.
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