MM and MD in SYBYL

Preface

In this tutorial, you will build and minimize ethanol, and do a molecular dynamics (MD) run ona a 'droplet' of ethanol.
After doing MD runs at different temperatures to see the effect on sampling, you will analyze a run on our protein-ligand complexes.

• Starting Sybyl
• Drawing a simple molecule
• Optimizing the molecular geometry
• Save structures to disk
• Running Molecular Dynamics on a droplet of ethanol
• Running Molecular Dynamics on a protein-ligand complex

Starting Sybyl

start Sybyl from your course account directory.

Sybyl should now start on your screen.

the Sybyl window is shown below, and consists of three areas:



1: the menubar
2: the toolbox icons
3: the main window

Finally, at the bottom of the screen there is the texport window.

• If necessary, clear all the molecule and display areas.

  From the menu bar, select BUILD/EDIT >>> ZAP (DELETE) MOLECULE
  If there is more than one molecule on the screen, click ALL, then OK to wipe them all.

• Reset your screen if necessary.

  From the toolbox, use the RESET gadget to reset EVERYTHING
  Use the DISPLAY OPTIONS tool to reset to FULL screen mode.

• Activate the sketch menu and select the first workarea in which to build the molecule.

  BUILD/EDIT >>> SKETCH MOLECULE...
  Select M1:<EMPTY> (press OK)
  
  
  
  When entering this mode, two menus appear: the 'Sketch Molecule Menu' and an 'Atomic Symbol Menu'. Your are placed in DRAW mode, automatically.

• Draw three carbon atoms:
  Pick a point in space in the middle of the screen.
  A highlighted cross appears, representing an unconnected atom. The highlight indicates that this atom is the point of attachment when a subsequent point is chosen as next atom. This is called 'continuous drawing mode'.

  Pick another point to the right of the first one.
  Pick the last atom, to the right of, and slightly higher than, the second one.
  
  
  
  

• Change C to O, and add hydrogen atoms:

  Select O from the atomic symbol menu, and click the last carbon atom you added. It should change color from grey to red, indicating it has changed into oxygen.

  Click ADDH. Hydrogens should be added to the molecule now, creating a C₂H₅OH molecule.

• Finally, bring the molecule closer to its normal conformation by clicking CLEAN_UP in the Sketch Molecule menu.

  Leave the Sketch Molecule menu by clicking End Select.

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  Optimizing the molecular conformation

  To optimize the molecular conformation, we will put atomic charges on the molecule and then minimize the energy.

• Add atomic charges to the molecule:

  To reflect the charge distribution on the molecule, Sybyl can put charges on the atoms. To do so, click Compute | Charges | Gasteiger. Because the molecule is electrically neutral, answer No if asked to assign a formal charge. The charges will be shown as atom lables:
  
  
  

• Minimize the molecular energy:

  First, put the molecule into a reasonable conformation by checking the C-C-O-H torsion angle, which should be around 180 degrees. If it is not, adjust it via Build/Edit | Modify | Torsion.

  Then, minimize the energy of the molecule.
  Set the correct energy function via Compute | |Minimize | Energy Setup: Modify... , and set Charges to Gasteiger-Marsili. Then optimize the structure by clicking OK in the Minimize window.

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  Saving the model to disk

• Name the molecule:

  Select BUILD/EDIT >>> Name Molecule... and type ethanol (press OK)

• Save the structure:

  Select FILE >>> SAVE AS... and type ethanol (press OK)

  A file 'ethanol.mol2' will be created. Note that the filetype is autmoatically added, and that the filename is case sensitive.

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  Running Molecular Dynamics on a droplet of ethanol

  Let's see how we can use Molecular Dynamics to sample the conformational space of ethanol.
  
  Zap (delete) the model of a singel ethanol molecule you just created, and load the model of a 'droplet' of 20 ethanol molecules available:

  File >> Read >> 20ethanol.mol2 >> OK

  Setup a Molecular Dynamics run:
  

  Compute | Dynamics | Setup Dynamics...

  Check the Energy setup to make sure atomic charges are used, and set the cut-off for non-bonded interactions (NB Cutoff) to 12 A.
  Back in the Dynamics window choose Intervals: Modify. Set the length of the simulation to 10ps, take snapshots every 50fs, and set the temperature to 100K.
  Back in the Dynamics window set the jobname to, e.g., MD100K, and hit OK. This will start the MD simulation, which should take a minute or two.

  Analyse the result of the MD run. One way to do this is to replay the MD trajectory, which has been stored during the calculations.
  Analyze | Dynamics | Replay Trajectory and select the appropriate file. See what happens!
  
  The ethanol molecules have two degrees of torsional freedom: The CH₃ group and the OH group can rotate. It is possible in Sybyl to see what happened to selected torion angles (or bond lengths or angles) during an MD run.

  Read in the trajectory file via Analyze | Dynamics | Analyze Dynamics. This will build a table containing data on a.o. energetics for each snapshot saved from the MD run. We can add a column for a selected torsion angle via: Edit | Insert | Column | Torsion ; now click four atoms defining a methyl-torsion in any ethanol molecule.

  Now create a plot of the torsion angle as a function of time: in the Table window, pick Graph | scatter, and select TORSION6 for the Y-axis. For the Z-axis, choose Omit AxisCreate, et voila!
  
  
  
  What can be concluded from the graph about the CH₃ torsional flexibility at this temperature? Do the same for a hydroxyl torsion.

  Now repeat the above procedure for a temperature of 400 K.

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  Running Molecular Dynamics on a protein-ligand complex

  
  
  A procedure simular to the one above can be used to sample configurations of a protein-ligand complex. Read in the structure of tamoxifen docked into the ER receptor by FlexX:

  File >> Read >> 3er-t-start.mol2 >> OK

  Wow, that looks like a mess!!
  
  To high/low-light certain parts or aspects of the structure, go to Biopolymer | Display | Backbone Only. Now, only the backbone of ER is displayed. To include tamoxifen, go to View | Display Atoms... | Substructures... and select the last entry, tamoxifen.
  If you want to highlight tamoxifen by giving it its own color, use the View | ... menu.

  Is this the optimal geometry of receptor and ligand? Probably not. An MD run has been carried out on this complex; to view the result, Load the file 3ert-200k.his into Sybyl, and describe what you see:

  Analyze | Dynamics | Replay Trajectory | 3ert-200k.his | OK

  Load the data for analysis: Analyze | Dynamics | Analyze Dynamics (except the defaults), which will load a table. Select the last frame, by clicking on the first element (501:R50000.000) of the last row, and load the structure into Sybyl via File | Put Row into Molecular Area.
  Note: it is important to select the last row, or else all structures will be loaded, which takes a long time!
  Optimize this frame.

  Finally, load the crystal structure of the complex, and compare it to the initial structure from FlexX, as well as the optimized structure you just created.

  As you have seen, not all atoms are moving in this model; only tamoxifen and atoms nearby it are. In fact, those are the atoms which are most interesting for us. To get a better view of the structure, you could do the following: Biopolymer | Display | C-alpha only. This leaves out just a bit too much, so next do View | Color | Atoms... | Sets... and select the last set, receptor.