Demonstrate Usage of gOpenMol for Molecular Dynamics Analysis

  1. start up gOpenMol by typing "gopen" 
     
  2. Main widget: File >> Import >> coords... 
     
  3. Import coordinates widget: Browse... 
     
  4. Read Coordinate File widget: click on crd file >> Open 
     
  5. Import coordinates widget: Apply >> Dismiss 
     
  6. Main widget: Trajectory >> Main... 
     
  7. Trajectory Control widget: Browse... 
     
  8. Trajectory file widget: click on dcd file >> Open 
     
  9. Trajectory Control widget: Import file 
     
  10. Trajectory Control widget: load the first frame by clicking [|<] 
     
  11. Main widget: View >> Atom mask... 
     
  12. Display Atoms widget: click 'Display state:' = "off" >> Apply 
     
  13. Display Atoms widget: click 'Use around:' = "on" 
     
  14. Display Atoms widget: type in "*" for the 'Segment:' and 'Residue:' boxes below 'Use around:' 
     
  15. Display Atoms widget: type in "7,11,18,21,29,34" for the 'Atom:' box below 'Use around:' 
     
  16. Display Atoms widget: type in "3.5" for 'Distance:' 
     
  17. Display Atoms widget: click 'Display state:' = "on" >> Apply 
     
  18. Trajectory Control widget: advance the display a bit by clicking |> and [] buttons in rapid succession 
     
  19. Display Atoms widget: update display by clicking Apply 
     
  20. redo steps 18 and 19 several times until it appears you have captured all atoms that range within 3.5 A of the H-bonding sites for the whole trajectory 
     
  21. Main widget: Trajectory >> Monitor >> Distance... 
     
  22. Monitor distance widget: enter "11" and "29" for 'Atom(s) #1: Atom:' and 'Atom(s) #2: Atom:' respectively >> 'Display:' = on >> Apply >> Dismiss 
     
  23. Main widget: Trajectory >> Fill >> Distance Array 
     
  24. Main widget: Trajectory >> Time Series 
     
  25. Manipulate Timeseries widget: 'Type of time series:' >> click on "distance" >> ABS >> 'Destination time series nr:' = 1 >> Apply 
     
  26. Main widget: File >> Export >> Timeseries... 
     
  27. Save Timeseries widget: 'Distance list #:' = 1 >> 'File name:' = test.dat >> Apply

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David Johnson
emaildkjohnson@ku.edu
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