Quick Guide to MacSpartan

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Medicine and the Biosciences Main Page

Table of Contents

• Controls
• Molecule Builder
• Menus
  • Model
  • Geometry
  • Build
  • Setup
  • Display
• Calculations: Hints and Troubleshooting

The very first rule to MacSpartan is: Don't have anything else running! These are PowerMacs, and they are wonderful tools, but MacSpartan will NOT run any calculations in a reasonable amount of time with anything else going on. Most of the time, MacSpartan won't even start a calculation with other applications running (the primary culprit here is Netscape... Don't even think about surfing while a calculation is running!). Also, be careful, if you make a molecule too large on screen (especially a space-filling model), MacSpartan can crash. So,

SAVE OFTEN!

Here is a short list of the most often needed keyboard/mouse commands:

Operation	Hold this key and mouse
Move on screen	Option
Rotate in plane of screen	Apple
Rotate bond	Spacebar
Zoom in/out	Option and Apple

Remember that your mouse can be used to select areas of the screen and rotate molecules in some directions. Back to top

Molecule Builder

The molecule builder is opened when you request a new file or when you edit the structure of an existing molecule. In the builder, you have a workspace (black) on the left, a floating toolbar, and a molecule kit on the right. This kit contains all the "pieces" that will be used for your molecules. There are two sections to the kit; "Entry", and "Peptide". We will only use the Entry part. The Peptide kit contains amino acids, used to build proteins (large biologicals). Since we are concentrating on ab initio methods, we will not deal with proteins. In the Entry kit, there are fragments representing common atoms, as well as "Groups" and "Rings", which are preassembled functional groups. We will deal with building molecule from fragments for the majority of our time.

Below are a list of common actions in the Builder

• To get started building a molecule, pick any fragment and click in the work area to deposit it. The ends of the bonds that it can form are highlighted; these are unfilled valences, or places that this fragment can bond.
• To attach another atom to it, select that atom, and then click on an unfilled valence.
• To match up two unfilled valences on atoms which are already on the screen, use the Make Bond item and click on the two valences.
• To erase a bond, use the Break Bond item and click on the bond.
• Use the Delete Atom item to remove a fragment.

Use the commands shown above to manipulate the fragments. Also, if you need more options, there are other commands under the Edit and Geometry menus of the Builder.

There are several fragments for some atoms, like carbon. This is because carbon can form different types of bond. Double or triple bonds are indicated by two or three lines on top of each other. MacSpartan automatically matches up multiple bonds.

When you are done making a molecule, click on Minimize. This will "bend" the molecule into a reasonable guess at the geometry.

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Menus

Model

• The options in the first section of the model menu are all different ways of displaying a model, different representations of a molecule. Try them to see what they look like!
• The "Hide Hydrogens" option does exactly what it says. This is primarily for large organics, where the hydrogens can obscure internal details of the structure. Once you hide the hydrogens, this option becomes "Show Hydrogens".
• The "Show Labels" option shows (and then hides) the labels that MacSpartan uses to name the atoms in a given molecule. These labels won't be very helpful to you.

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Geometry

• Distance-pick two atoms (or a bond) to find the distance between them in Angstroms
• Angle-pick three atoms to find the angle between them. Careful! The order of the atoms matters. The second atom is the vertex of the angle.
• Dihedral-pick four atoms to find the dihedral angle between them. The first three atoms are used to make an imaginary plane, and the angle between that plane and the fourth atom is the dihedral angle.
• Define Point or Plane-these are extra tools to analyze the geometry. The point in the center of a group of atoms or a plane defined by certain atoms can be defined and used to measure other quantities.
• Report Symmetry-this give a technical definition of the symmetry of the current molecule

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Build

• Edit Structure-this returns you to the Builder with the current molecule in the work area. Molecule Builder help
• Transition Search-must have both reactant and product on screen to do a search for transition states (intermediary products). Last molecule clicked on is automatically used for reactant.
• Isotopes-lets you specify a different isotope of any atom by clicking repeatedly on that atom. Most common isotope is automatically used.

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Setup

• Calculation
  • Task-choose from Single Point Energy, Geometry Optimization, Transition Structure, Frequency as needed. See glossary for a definiton of these terms.
  • Level-choose type of theory and basis set
  • Charge-should be 0 (unless you are working with an ion!)
  • Multiplicity-should be 1
  • Options-use this box to modify the parameters MacSpartan uses. Entering "nosymtry" (without quotes) will cause MacSpartan to ignore molecular symmetry. Entering "optcycle=500" will cause MacSpartan to use 500 iterations (instead of the standard 250) before it gives up on an optimization.
• Surfaces-almost all of these options are available either as separate surfaces or as properties of another surface. If one is displayed as a surface of its own, MacSpartan calculates the distance from the molecule where this quantity has a certain value all over; this makes up the surface. If it is a property of another surface then that surface is calculated as usual, but red/blue shading is used to display the value of the property over that surface. See glossary for a definition of these terms.
  • Electron Density
  • HOMO
  • LUMO
  • elpot (electrostatic potential)
• Submit-Perform the selected calculation. Make sure nothing else is running!

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Display

• Output-a simple dump of the output (alphanumeric) of the engine used.
• Properties
  • Energy-the energy of the molecule, as calculated in the last run
  • Dipole-the dipole moment is displayed and the vector is drawn on screen
  • Charge-gives the electrostatic and Mulliken charges of any atom
  • Surfaces-will measure the value of a property displayed on a surface
• Surfaces-a dialog box for displaying surfaces and properties of surfaces
• Frequencies-a dialog box for showing the molecular vibrations corresponding to various frequencies. This animates the molecule onscreen. To deactivate the animation, use this dialog box again.

Be careful- if you define a new calculation and MacSpartan gives you a dialog box which says it will require "regenerating the wavefunction" etc., that means that you will not be able to display the results of the last calculation.

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Calculations

Hints and Troubleshooting

• If a dialog box comes up saying that a calculation can't start because there isn't enough free memory, see rule #1 of MacSpartan! Close everything else and try again!
• A window will come up during calculations which displays the calculation and the time it has taken so far.
  • File menu-lets you open and close this window. Quitting causes all jobs to be suspended-so don't use this option.
  • Actions menu
    • Set Job Speed-use this slider bar to accelerate MacSpartan. It means that you can't run anything else on the Mac, but hey, you weren't going to do that anyway! The Mac spends almost all of its time thinking about MacSpartan instead of other stuff. Do this whenever you have a job running.
    • Kill-"This function will gracefully terminate the selected task." Do this when you made a mistake or are sure that the job will blow up anyway.
• ALWAYS ALWAYS do a geometry op before a frequency calculation!
• If your job blows up after a lot of calculation, but doesn't seem to have anything wrong other than that, try increasing the optcycles. See Setup to learn how. Also try minimizing it under the Builder to give the geometry a running start.
• Read the dialog box that MacSpartan gives you if your job blows up. It's trying to tell you something! Think about what the described problem means.
• Ask for help if you need it!

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