Output - Advanced Settings Dialog Box DEPRECATED

Output - Advanced Settings Dialog Box Features

• Filter section
• Clustering section
• Strain correction section
• Keep subjob poses option

Filter section

There is one option in this section:

Reject poses with Coulomb-vdW energy greater than x kcal/mol

If the pose has a Coulomb-vdW score greater (more positive) than this value, the pose is rejected. The default value is 0.0 kcal/mol. This means that poses that interact favorably with the protein site, however weakly, are retained, whereas poses that interact unfavorably are rejected. Change x to a negative value to reject poses with weakly favorable interactions, or to a positive value to keep poses with mildly unfavorable interactions.

Clustering section

The clustering options determine which ligand poses are sufficiently alike to be considered duplicates. Ligand poses are compared to those previously selected for inclusion in the output, and are discarded as duplicates if either of the following criteria are met. This ensures that reported poses are conformationally distinct. The criteria are:

RMS deviation is less than rÅ

A pose is considered a duplicate if its heavy-atom (nonhydrogen) RMS deviation from any of the poses already included is less than r Å. The default RMS deviation threshold r is 0.5 Å.

Maximum atomic displacement is less thandÅ

A pose is considered a duplicate if the maximum atomic displacement for any atom is less than d Å. The default is 1.3 Å.

Include hydroxyl/thiol torsions D degree

A pose is considered a duplicate if, in addition to satisfying the maximum atom displacement criteria, the difference in the dihedral angles involving hydrogen bonds to rotatable hydroxyl/thiol torsions in the ligand is less than the specified amount. If a difference in dihedral angle exceeds this amount, regardless of the criteria involving only the distances, the pose is not considered a duplicate.

Strain correction section

The GlideScore is corrected for excessive strain of the ligand by adding to it a fraction of the strain energy that exceeds a threshold value. This correction is made only if you have selected Apply strain correction terms in the Output tab of the Ligand Docking panel.

Threshold for strain correction text box

Enter the threshold for applying the strain correction in this text box. The threshold value is subtracted from the strain correction before it is added. Values of the strain correction that are smaller than this threshold are not added to the GlideScore. The default threshold value is 4.0 kcal/mol.

Scaling factor for excess strain energy text box

Enter the factor that multiplies the excess strain energy in this text box. The excess strain energy is the strain energy minus the threshold value. The default scaling factor is 0.25.

Keep subjob poses option

Keep the zip archive, jobname_subjob_poses.zip, which contains the pose files from all the subjobs of a distributed docking job. The archive is copied back to your working directory along with the other output files. This archive may be useful if you limit the number of poses to report for the job too severely and want to examine other poses without doing the entire docking run again. You can run glide_merge using the contents of this archive with the -n option to set a new number of poses to report. If disk space is an issue, you might want to deselect this option.