1. Read in the molecule.

2. Add any hydrogens you consider appropriate, as usual.

3. Select it as the ligand using Ligand->Input->Choose...

4. Set the picking level in the viewer to Atom if necessary:

    -click on the Picking COMmands button in the Tool Bar ('pointing finger' icon, 5th from left)

    -click on the picking level: molecule- to display a drop-down list of levels.

    -select Atom in this drop-down list

5. For each bond you want to force to be treated as rotatable:

    A. Select the two atoms involved in that bond using the Picking Command and ONLY those two atoms:

       1. If there is anything selected in the viewer, clear selection first using the Clear Selection button ( 'eraser' icon, 4th from left)

       2. Place the cursor over the first atom

       3. While holding down the Shift key, click with the left mouse button

       4. Place the cursor over the second atom

       5. While holding down the Shift key, click with the left mouse button

    B. If necessary, open the python shell by clicking on the Python IDLE Shell button ('whitish box' icon, 6th from left)

       1. type each of these lines at the Python prompt which is >>> followed by pressing the Enter key

          b = self.getSelection().bonds[0][0]

          b.possibleTors = 1

          b.activeTors = 1

    C. Clear the selection before processing the next bond by clicking the Clear Selection button ('eraser' icon, 4th from left)

After you have processed all the bonds you want to force to be rotatable, continue processing the ligand as usual....

6. Ligand->Torsion Tree->Detect Root...

7. Ligand->Torsion Tree -> Choose Torsions...

8. Ligand->Output->Save as PDBQT