Using Nanocad

Tutorial - Use Nanocad & Create Gaussian input

1. Navigation to Nanocad editor (From top menu): Molecular Editors → Nanocad
2. After Nanocad has launched, take your time to read text "Summary of Nanocad Commands" at the top of Nanocad window (Indicated by the green box in Image I). 
   
   1. You will get basic idea how to use Nanocad
      
      Image I - Nanocad Editor 
3. If there is an example water structure in the Nanocad window, to erase this click the Clear button. 
4. To build a new structure, you need to click the STRUCTURE button at the bottom of the Nanocad window.
   
   1. A new small window with the title Import Structure will pop up on top. (Hint: Move the Nanocad window slight below the Import Structure panel so both are visible simultaneously)
      
      Image II - Import Structure Pop-up Window
5. Go to Database → CSD
6. Search for 'Norbornane' and double click 'C9 H12 O4'.
7. The molecule will appear on the editor and to center the molecule ctrl + click on the empty background space area (not on the atom).
8. Ctrl + move the moues to enlarge the molecule.
   
9. From Input/Oputput Menu at the right bottom select, Gaussian input.
10. A pop-up message, 'This will open a Gaussian GUI, and the current molecule ..........' say Yes.
    
    Image III - Message Pop-up Window
    
11. A Warning message 'WARNING:Molecule information has been exported correctly..........' will appear and say, Yes.
12. Opens Gaussian 09 Input GUI.
13. Click View/Edit Structure button and it opens the molecule structure of the exported molecule.
14. Select Save/DisplayMol from Molecule Specification →File menu.
15. Then the molecule will be displayed in the main Gaussian 09 GUI.
16. Close the Molecule Specification window.
17. Select Method --> DFT-> Common Hybrid Functionals→B3LYP.
    
    Image IV - Select Wavefunction Type
    
18. Opens 'Select Wavefunction Type' select 'R - Restricted closed - shell'.
    
19. In the Gaussian 09 Input GUI → Route Section you should have # RB3LYP. You would see the same under Methods in the window on top left hand side with tree structure.
20. Select, Basic sets → Frequently-used basis sets → 6-31G. Say 'Yes' to Add Polarization d and/Or Diffuse Function.
21. In 6-31G options set, Sets of d functions on Heavy atoms and Sets of p functions on H atoms to 1.
22. Select 6-31+G in Diffuse functions.
23. Now in Route Section you would have # RB3LYP/6-31+G(d,p) 
24. Select Job-types → Commonly-used job Types → Opt.

25. In Opt options, click 'Done' (no need to select any options).

26. In Route Section you would have: # RB3LYP/6-31+G(d,p) Opt 

27. Select Keywords → Common Keywords → Pop. In Pop options select 'Reg' and say done. Route Section should have # RB3LYP/6-31+G(d,p) Opt Pop=(Reg).

28. Select Keywords → Other Keywords and select GFInput, GFPrint and IOp options. In Iop options give Overlay - 6, options - 7, Value - 3. Now Rounte Section will have # RB3LYP/6-31+G(d,p) Opt Pop=(Reg) GFInput GFPrint Iop(6/7=3).

29. Hint: Below in Help section you would be able to view all the descriptions of each keyword selected and displayed in the tree structure on left top.

30. In Gaussian 09 Input GUI, set %nproc - 24, %mem(in MB) - 2000
31. Provide a checkpoint file name, norbornane.chk
32. Job Title & Description: Norbornane di carboxylic acid RB3LYP/6-31+G(d,p) Opt Pop=(Reg) GFInput GFPrint Iop(6/7=3)
33. Add charge = 0, multiplicity = 1.
    
34. Click Done & Export button.
35. Create Experiment window will open with the created Gaussian input and with already defined exp name and description.
36. Select bridges.psc.edu to run and RM-Shared queue.
    
37. Save & Launch the experiment.