In the tarred source distribution of molden5.8 there are examples of
three dockings in the directory test/dock.
Go to the directory
4dfr and load the file 4dfr.pdb into Molden.
Click the BackBone button to reveal the secondary structure of the protein.
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Click the HetAtm button to display the methotrexate (MTX) ligand.
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Click with the middle mouse button on the methotrexate ligand on screen
to bring up the HetAtm Menu and select the Center option.
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Click the align icon in the Molden command window and select the
Incremental Docking option.
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Read the instructions in the Molden OK box and click OK.
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You will specify a volume in which the amino acids are assigned interaction points.
These interaction points belong to basically three classes:
Hydrogen bond acceptor
Hydrogen bond donor
Lipophylic/Aromatic
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After hitting the escape button, the Docking Start window will pop-up.
You will need to specify an ambfor .xyz file containing the ligand you would like to dock.
Click the File icon. The Molden File Select window will pop-up.
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Click the "dtst.xyz" file (contains a part of Methotrexate) and click the OK button.
Click the Dock ! button to start the docking.
During the docking the Cursor will be displaying a busy animation.
When the docking is finished the cursor will change back to the default arrow.
The results of the docking will be stored in a .mol2 file you specified in the
Docking Start window, default Dock.mol2.
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Click with the middle mouse button on the methotrexate ligand on screen
to bring up the HetAtm Menu and select the Contacts+Surf option.
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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.
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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.
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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).
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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.
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Finally we can make some optical changes to increase the visibility of the docking poses:
Click the Solid button in the Molden Control window and select the sticks option.
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Click the Palette icon in the Molden Control window and select the shadows option.
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