Intro to gOpenMol

gOpenMol v1.0A1

a freeware package created by:
Leif Laaksonen,Center for Scientific Computing
Capabilities
  • Molecular Images
    (stick / ball & stick / space-filling)
  • Contour Plots
  • Contour Cutplanes
  • Trajectory Animation
  • Output to *.ps, *.bmp, *.rgb, *.tga, *.xwd
  • Orthographic and perspective projections
  • Superimposition of multiple isosurfaces
  • Prototype analysis tool for AutoDock trajectories
Hardware Platforms
  • DEC Unix (MESA)
  • IBM AIX (OpenGL and MESA)
  • PC/Linux (MESA)
  • SGI IRIX (OpenGL and MESA)
  • Windows 95 and NT (WIN32)
Compatible File Formats
  • Amber
  • Cerius2
  • CHARMm/CHARMM **
  • Discover
  • Gaussian **
  • Gromos
  • Hyperchem
  • Insight
  • Mol2
  • Mumod
  • OpenMol
  • PDB
  • Tinker
  • Xmol **
  • XPLOR
  • XYZ
  • YASP

Example 1
2-benzyl 4-ethoxymethyl oxazolinic ester Oxaz
  • Type "gopenmol" to initiate program
  • File: Import: Coords:
  • Select "Charmm"
  • Browse: select "oxaz.crd"
  • Open and Apply
  • View: Atom Type: CPK

 

 

 

Example 2
Contour and Cutplane for Napthalene
  1. File: Import: Coords:contour and cutplane
  2. Select "Gaussian"
  3. Browse: select "napth.FChk"
  4. Open and Apply
  5. Run: gCube2plt:
  6. Input file: Browse: select "napth.data"
  7. Output file: select "napth.plt"
  8. Apply
  9. Plot: Contour: File name:
  10. Browse: select "napth.plt"
  11. Open and Import
  12. Plot: Cutplane:
  13. select "XZ-plane" and apply
  14. select "YZ-plane" and apply
  15. YZ-plane: set coord to "1.21"
  16. Plot: Contour Scale:
  17. Set max to "0.3", display to "on", and Apply
  18. Plot: Cutplane:
  19. Set Max to "0.3" for XZ and YZ, and Apply
  20. File: Reset: gOpenMol
Example 3
  1. Trajectory Animationhydrogen above metal surface
  2. File: Reset: gOpenMol
  3. File: Import: Coords:
  4. select "Charmm"
  5. Browse: select "gas_surf.crd"
  6. Open and Apply
  7. Plot: Colour scale: set Display to "off"
  8. Edit: Edit molecule: Break bonds:
  9. click on screen
  10. Trajectory: Main: select "xmol"
  11. Browse: select "gas_surf.xmol"
  12. Open, Import and Apply
  13. Play ( |> )
  14. View: Atom Type: CPK
  15. Apply

CONTACT
David Johnson
emaildkjohnson@ku.edu
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