| GRID manual | ||
|---|---|---|
| <<< Previous | Next >>> | |
Chapter 51. Greater tutorial 04
51.1. A single small molecule example
In the first and second worked examples we studied a protein Target (file PDB.pdb) which was supplied as ATOMS in PDB format. In the third example we studied a list of protein Targets. Now we will look at the morphine molecule in file morphine.mol2 which is in Tripos Sybyl format.
Morphine.mol2 would be unacceptable as input to Programme GRIN which must have input files in PDB format. We must therefore use Greater in order to change the format and the atom names.
Go from the your working directory in the Tutorial04 directory:
cd Greater04
Type Greater as usual
The first thing to do is adding the morphine target molecule for the computation; to do that select:
Targets->Add single target (or press the Add Single button).
Now insert morphine.mol2 in the File name box shown below:
and press the OK button.
A new line will appear on the Greater window with the morphine.mol2 file and status "in progress" until it turns to "ready". Notice the additional information provided in the Greater window like the charge of the imported molecule that will be +1.0.
After the GRIN run, the User should check if anything unexpected happened during the .pdb - .kout conversion; this time the procedure was completed without warnings or errors. Click on the morphine.pdb line with the right mouse button and select view text files to check the output or select view structures to inspect graphically the 3D structure of morphine.
Please note that some new files were created by Greater in the greater04 directory. They are the morphine.kout and morphine.lout. The .kout contains all the parameters required by GRID force field.
51.1.1. RUNNING THE PROGRAMME GRID
Before running GRID as usual we need to set some options from the interface: the first thing is to define the type of probe which is to be used by GRID. To do that select:
Probes->Choose probes from the menu (or press the Probes button) and the usual probe window will appear.
Select the OH (hydroxyl) probe clicking on its name so the "selected" column reads "IN" and press OK.
Choose, in the "box" section, NPLA. Select 3 as input value modifying the default value; press OK to confirm.
Now select:
Compute->Run (or press the Run button) and choose from the following window:
visualise fields
then press the OK button to actually start the GRID run.
51.1.2. ASSESSING THE RESULTS FROM PROGRAMME GRID
The status bar of the Greater main window will report "running" and after few seconds will turn to "Completed". Once the GRID computation will be completed and the map is generated the Targets->View fields command becomes active along with a new tab in the Targets->View text files window containing the GRIDLONT output.
Now we are ready to visualise the GRID map graphically; select the
Targets->View fields command (or press the View button) and the GVIEW programme will start.
The Molecular Interaction Field produced by the hydroxyl probe will be reported on the screen together with the morphine molecule (if the molecule will not be reported, please use the commands:
File->Open and then select the morphine.mol2 from the dialogue).
The yellow region refers to interaction energies between hydroxyl probe and the morphine. This contour level has been automatically selected by Gview programme.
To change the energy levels,select:
Edit->Field style
Move the cursor of the interaction energy levels up to -3.5.
Then you can move the image pressing the left button of the mouse and moving the mouse at the same time.
Graphic interpretation shows that there is a ring-shape interaction region around the hydroxyl group of morphine and a banana-shape interaction around the morphine phenolic group. Is the spatial distribution of hydrogens and lone pairs and their spatial flexibility that generate such maps.
Try to import a flexible molecule, and set the MOVE directive to 1.0. Reproduce the computation and try to interpret the results. See MOVE directive in the manual for help.
You have now completed your fourth Tutorial. Well done!! We look forwards to hearing from you if we can help in any way.
Please, continue with Tutorial05.
| <<< Previous | Home | Next >>> |
| Greater tutorial 03 | Up | Greater tutorial 05 |