TD d’Informatique

MANIPULATIONS WITH THE SOFTWARE MOE.

1. Building the start structure:

Builder

Drawing

  • Click on a cycle, group or element symbol to add it to the main MOE window.
  • Select an atom (click on it) then click on a cycle, group or element symbol to append it to an existing structure
  • Select two bonded atoms, and then click on a bond type button to modify the bond accordingly.
  • The Delete mode will delete any atoms selected or subsequently clicked on.
  • The Minimize button will relax the conformer on screen following the steepest descent in energy. By default the molecular force field used is MMFF94x.

Read structures from files

  • File -> Open(select the name of the file to be opened). Look carefully on the right part of this interface: structures shall be loaded on the MOE interface. Alternatively, it can be stored into a MOE database but this operation is better used for chemoinformatics tasks or structured projects.

Create a conformer

  • Click on 2 bonded atoms while the Build menu is open. A frame in the build menu is activated that allows adjusting the bond length between these atoms
  • Click on 3 bonded atoms while the Build menu is open. A frame in the build menu is activated that allows adjusting the bonds angle defined by these atoms
  • Click on 4 bonded atoms while the Build menu is open. A frame in the build menu is activated that allows adjusting the dihedral angle defined by these atoms

Hydrogen

  • Two buttons allows adding or removinghydrogen. They are added so to complete missing valences.

View

  • The structure can be rotated or zoomed using the wheels displayed at the bottom of the main MOE window
  • Middle click on the main window allows forrigid rotations freely with the mouse
  • Ctrl+Middle click allows to control the zoom with the mouse
  • Shift+Middle click allows for rigid translation of the structure
  • The Mode menu allows to select for various molecular representations
  • The Label menu allows to select which information are to displayed on an atom (or residue) basis on the structure
  • The Color menu allows to play with different colorations of the structure to emphases parts of what is displayed on screen

2. Energy calculations.

You shall select the appropriate force field to use before any further calculations

Edit  Potential Setup

Compute

Energy calculations of a conformer.

ComputeEnergy Minimize

A parameterisation window opens:if all settings are correct click on OK. Force field parameterization can be setup at this point by click on Force Field.

Torsion drive.

ComputeMechanicsDihedral Energy Plot

Two angle torsion drive

ComputeMechanicsDihedral Contour Plot

Display electrostatic charges.

Charges must be calculated or loaded from the force field

ViewLabelCharges

The electrostatic map can be calculated through

Compute Surfaces and maps

Then select Surface: Electrostatic Map, Atoms: all atoms, Near: all atoms and click Apply.

Maps can be deleted using the interface in Window Graphic Objects

Constrains.

Select atoms that shall not move (2 atoms to constrain a bond, 3 for angle, 4 for a dihedral)

ComputeEnergy Minimize

In the parameter window tickTetherAtoms: Selected then click on OK.

Alternatively, invert your selection (Selection Invert) and in the parameter window, tick Selected Atoms Only.

Molecular Dynamics

MDat room temperature

ComputeSimulationsDynamics

A parameterization window opens, give a name to your simulation in the Database field, keep all other parameter values to default and click OK.

MDat high temperature

ComputeSimulationsDynamics

A parameterization window opens, give a name to your simulation in the Database field, and set the temperature in the field T. Parameterize heating procedure (length of heating, length of production calculations, heat control, and temperature increments) and then click OK.

3. Analysis of calculation.

Simulations results, stored conformers and thermodynamics values for each of them are stored into a database. Analysis is done through the interface of the MOE database.

Visualization of conformers

Animation and display of the database content into the MOE interface is done through the browser:

File Browse

Alternatively any number of conformers can be selected in the database. Then right click on the mol field that contains the conformer and choose in the contextual menu Send selected to MOE. Selected conformers are overlapped in the MOE main window.

Geometry of conformers.

Compute  Conformation Geometry

Then select 2, 3 or 4 bonded atoms according to which measure of bond length, angle or dihedral shall be recorded. Conformers can overlapped and RMSD to the conformer in the MOE window will recorded in the same interface.

DisplayPlot

Adds a frame to the MOE database interface in which recorded quantities or calculated properties on each conformer are represented as function of time.

Ramachandran maps:

Compute  Conformation Geometry

And define two dihedrals as required for a Ramachandran plot

ComputeAnalysisCorrelation plot

This will open a new display window for dispersion plots.

Into any plot area, it is possible to draw a rectangle to select one or several points on the plot: the corresponding structures are selected on the database. The database Browser has a tick box to display only selected entries in the database.

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