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How do I install Spartan for Linux?

Click Here to Open Installation Directions for Spartan for Linux Installation Directions (pdf file)

How do I import files from other modeling programs? What file types does Spartan recognize?

In the current Linux version of Spartan, file import is managed via the File Menu - Import option. Spartan for Linux recognizes several molecule file types, including:

Standard Spartan file formats (Spartan Exchange and Spartan Collection)
Published .smiles (1-D) files
SKC, TGF, and SD/SDF (2-D) files (MDL file formats)
Additionally, 3-D file import is available for MacroModel, Sybyl Mol and Mol2, PDB, CIF, and XYZ files

How can I quantify molecular geometries?

To query the numerical values of any bonded or non-bonded distance, angle or dihedral (torsion) angle, choose from the Geometry Menu:

Measure Distance - Select (by clicking) either a bond or two atoms to measure distances, distance appears in the lower right hand corner and can be 'Posted' to the spreadsheet by clicking on the P icon next to the distance
Measure Angle - Select (by clicking) either two bonds or three atoms to measure an angle (note the selection order matters), the angle value appears in the lower right hand corner and can be 'Posted' to the spreadsheet by clicking on the P icon next to the angle
Measure Dihedral - Select (by clicking) either three bonds or four atoms to measure a dihedral (torsion angle), the selection order matters, the dihedral angle value appears in the lower right hand corner and can be 'Posted' to the spreadsheet by clicking on the P icon next to the dihedral angle

Note: Queries may also be made between user defined points or planes.

What does the Minimize Energy button do?

The Minimize Energy button/icon is used to reduce the strain energy of a molecule during the building process and typically upon completing the construction of a molecule. This button is a shortcut to performing an Equilibrium Geometry calculation using the MMFF (Merck Molecular Mechanics Force Field) and attempts to:

Minimize distortion from parameterized "ideal" bond distances and angles
Optimize geometry with respect to non-bonded van der Waals interactions
Optimize geometry with respect to Coulombic interactions

Note: MMFF94 was parameterized for common organic molecules, the Minimize Energy function produces a local energy minima for organic molecules, but may produce undesirable results for molecules with metal atoms.