Here we explain how to re-position a ligand independently of other molecules using ADT/PMV. Note that AutoDock moves ligands inside a grid when initial position of a ligand is outside of bounding box.

Step 1) Click on DejaVu GUI icon () on the Toolbar.

Step 2) Select molecule of interest in "DejaVu GUI" window under Object tree. In this example, the molecule we are moving is called "HIS".

Step 3) Click on Preferences menu in "DejaVu GUI" window and uncheck "Transf. Root Only" radio button. This now allows molecules to be moved independently of one-another.

Step 4) Re-position molecule in 3D Viewer. See "Basic key and mouse bindings"

Step 5) Select the molecule you have re-positioned in the dashboard of PMV. This is required since PMV can save only one molecule at a time. If you have none selected, it assumes that all are selected.

Step 6) Save transformed coordinates using "File → Save → Write PDB". Make sure to click on "Save Tranformed Coords" radio-button in "Write Options" window, otherwise ADT saves the original, un-transformed coordinates.