Molecular docking with Molden in 16 steps

In the tarred source distribution of molden7.2 there are examples of dockings in the directory test/dock.
Go to the directory 4dfr and load the file 4dfr.pdb into Molden.
Go here for a step by step recipe of docking with molden versions 7.1 and lower.

Click the BackBone button to reveal the secondary structure of the protein.

Click the HetAtm button to display the methotrexate (MTX) ligand.

Click the "Align" icon and select the "Incremental Docking" option.

The Docking Start window will pop-up. You will need to specify an HETATM position you will be using as docking site.

Use the first MTX record.

Next we need an AMBFOR .xyz file (with hydrogens) of the ligand to dock. Click the "mtx.xyz" file (contains Methotrexate) and click the OK button.

Next we need to select the "Quality" docking/

Click the Dock ! button to start the docking. The results of the docking will be stored in a dock.mol2 file (if you did not change it).

Click the Solid button in the Molden Control window and select the sticks option. Click with the middle mouse button on the methotrexate ligand on screen to bring up the HetAtm Menu and select the Add Hydrogens option. Click with the middle mouse button on the methotrexate ligand on screen to bring up the HetAtm Menu and select the Contacts+Surf option.

Two windows will pop-up: In the Molden Calculate window, click the Clear Mon/Cont button. In the Create Surface window, click the Map Electrostatic Pot. button. Followed by a click on the Create Surface button.

Now we are ready to read in the docking results .mol2 file. Click the Read button in the Molden Control window. In the Molden File Select window click the Add button. Read the message in the Molden OK Box and click the OK button.

Optionally you may supply a filter, to restrict the number of files being displayed. Now select the .mol2 file containing the docking results (default dock.mol2).

The Multi-mol file window will pop-up containg three poses: the force field scoring is displayed for each pose. In addition the first docking pose is displayed overlaying the Methotrexate ligand from the crystal structure. Finally we can make some optical changes to increase the visibility of the docking poses: Click the Palette icon in the Molden Control window and select the shadows option.