J. Liu, 2011.5.17

1. Install VMD
2. Unzip msms_win32_2.6.1
3. Copy msms.exe to ../University of Illinois/VMD
   (We will call /VMD the diretory of VMD where you
    can find all VMD files.)
4. Make a new directory called /GA 
   (to put all your data files about 
    the Gramicidin A (GA) channel).
5. Start VMD (you will get 3 windows.)
6. In the "VMD Main" window, choose 
   "Extensions -->  Data --> PDB Database Query"
   and the window "VMD PDB Tool" will appear.
7. In PDB Accession Code, type "1MAG" (this is the
   code name of GA) and download it to /GA.
   (You can see the loading process in the vmd.exe
    window and see the file 1MAG.pdb in /GA.)
8. Open the webpage 
   "http://kryptonite.nbcr.net/pdb2pqr/"
9. In the botton "a PDB ID:", enter "1MAG",
   click "CHARMM" botton and 
   then click the "Submit" botton.
10. The webpage will give you an output file 
    1MAG.pqr. Download it to /GA.
11. In the "VMD Main" window, choose 
    "File --> New Molecule" and the window 
    "Molecule File Browser" will appear.
12. Browse the file 1MAG.pqr and click "Load".
    In "Open GL Display" window, you can see the
    3D picture of 1MAG.pqr.
13. You can use mouse to play with the piture 
    for a while.
14. In the "VMD Main" window, choose 
    "Graphics --> Representations" and a new window 
    will appear.
15. In "Drawing Method", choose "MSMS".
    In "Sample Desity", choose 7.
    In "Probe Radius", choose 1.3.
    (Now you can see a hole in the piture. 
     That is the channel.)
16. Choose "Display --> Axes --> Off".
    Choose "Graphics --> Colors" and
    a new window will show.
17. In "Categories" choose "Display".
    In "Names", choose "Background".
    In "Colors", choose "8 white".
    (See what happens to the picture.)
18. In "Extensions --> Visualization",
    choose "Color Scale Bar".
    In the new window, set -10 in
    "Minimum scale value", and 10 in
    "Max...". Choose "black" in "Color
    of labels".
    Choose "Decimal" and click
    "Draw Color Scale Bar".
19. Save the picture by ¤pµe®a.
20. Done.