Spartan for Linux
Frequently Asked Questions
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How do I install Spartan for Linux?
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
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.