you just need to open the file .mgz in the working directory. it will automatically open in the project table.

 yes, for open the output docking file. but i have 10.000 molecules. and i would keep the best ligands for my homology modeling protein. top molecules of docking xp protocol not are also the best in mmgbsa protocol final score.

You have to select the number of poses for the ligand as 10. You will get the top 10 poses of the ligand. You can then superimpose the obtained poses on the native ligand and find the 1 that overlaps with the native ligand and the one that shows maximum number of interactions as shown by the native ligand.

All the best

You can select the protein and the poses you are interested in in the "Project table" and then duplicate it into group. Then you can save it as a .mae file. When you have it in *.mae you can use it further on.

Jacek

I know it is an old question, but I got here looking for a similar case so I thought I'd add the best answer I could find. Maybe it can help someone in the future...

You can use the Schrodinger utility "glide_sort" to extract only the best poses, using any criteria you want. For example, given you have a poseview file (docking poses + target protein) named "docking-results_pv.maegz", you can extract the top500 poses by:

```

$ $SCHRODINGER/utilities/glide_sort -o best500-XP_pv.maegz -n 500 docking-results_pv.maegz

```

This will create a new file (best500-XP_pv.maegz) with only the top 500 poses.