Building Gramicidin A

Arrange Lipids

This is the most exciting step! Here is where we actually pack the protein and lipids together.

Arranging the protein is up to you. After you run this step, you'll have a VMD session with the newly built lipid bilayer showing only the phosphate atoms, and the protein. Position the protein as follows:

1. Switch to Move Molecule mode by moving the mouse into the graphics window and pressing the 8 key. The cursor should now have the form of a cross-hair.

2. While holding down the shift key, click on one of the protein atoms and drag the mouse. You should see just the protein rotating around the atom you picked. Try to align the axis of the protein with an imaginary line coming out of the screen, so that it's perpendicular to the membrane. If you accidentally rotate the whole scene instead of just the protein, type "display resetview" in the text console to get back to the original view.

3. Type "rotate x by -90" in the text console. Now you want to center the protein between the phosphate atoms of the bilayer. This time, click and hold on one of the protein atoms _without_ holding down shift. Move the protein up and down until it's centered.

4. Switch back to the orginal view with "display resetview". If the protein looks good, you can go on to the next step; otherwise repeat steps 2 and 3 above.

Run this step!     Continue 

arrange_lipids.vmd

# STEP 3: Arrange POPE

mol delete all

mol load psf pope.psf pdb pope_move.pdb 
global popemol
set popemol [molinfo top]
mol load psf protein.psf pdb protein.pdb

display projection orthographic

mol modselect 0 $popemol "name P"
mol modstyle 0 $popemol VDW

puts {
        1. Switch to Move Molecule mode by moving the mouse into the graphics
           window and pressing the 8 key.  The cursor should now have the form
           of a cross-hair.

        2. While holding down the shift key, click on one of the protein atoms
           and drag the mouse.  You should see just the protein rotating
           around the atom you picked.  Try to align the axis of the protein
           with an imaginary line coming out of the screen, so that it's
           perpendicular to the membrane.  If you accidentally rotate the
           whole scene instead of just the protein, type "display resetview"
           in the text console to get back to the original view.

        3. Type "rotate x by -90" in the text console.  Now you want to center
           the protein between the phosphate atoms of the bilayer.  This time,
           click and hold on one of the protein atoms _without_ holding down
           shift.  Move the protein up and down until it's centered.

        4. Switch back to the orginal view with "display resetview".  If the
           protein looks good, you can go on to the next step; otherwise repeat
           steps 2 and 3 above.
}