I would like to export just the ligands from an Induced Fit docking output file. How do I do this?

You can use the pv_convert.py script for this task. This is a command-line script that is available from the Script Center in the Docking/Docking post-processing section, http://www.schrodinger.com/scriptcenter/#Docking, under Create or Convert Pose Viewer Files. This script can convert pose viewer files into a series of complexes, and convert complexes into ligand-only, receptor-only, or pose viewer files.

To separate out the ligands in the Induced Fit output file, run the script as follows:

$SCHRODINGER/run pv_convert.py -l jobname-out.maegz
 

This command writes all the ligands to individual files:

jobname-out_1_lig.maegz
jobname-out_2_lig.maegz
jobname-out_3_lig.maegz
...

You can then concatenate these files, if you would like all ligands to be in a single file. For example:

cat jobname-out_*_lig.maegz > all_ligands.maegz

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