Chapter 3-Building a unit.

NAMOT2 allows the user to build non-standard units and keep them in the unit library. This is done by reading in the bases as rigid bodies, manipulating them, writing them out, then reading them back in with the right pairing file.
There are two methods of manipulating the bases.

By Hand

  1. Create a pdb file for the bases you are interested in. The base must already be defined in the base library. If it isn't, you will need to add the base to the library.
  2. Delete the current molecule.
  3. Load the files as rigid bodies.
    Example:load pdb rigid gua.pdb
  4. Change the mouse mode to "Base".
  5. Use the mouse to rotate and position the bases. Also use the mouse to set up distance monitoring.
  6. Write out the file in pdb format.
    Example:write pdb ug.pdb
  7. Edit the file to remove the "ENDMDL" records, except for the last one.
  8. Produce the pair file.
    1 2
    1:1:1:1:nwc 2:1:1:2:nwc
  9. Delete the current molecule.
  10. Load in the unit file.
  11. Write the unit into the library file. This command can be found in the Write section of the command reference

By Geometry

If the information for two of the hydrogen bonds between two bases is known, you can use this information to make the unit.
  1. Place the bases in the correct Alpha face orientation using the rotate command.
  2. The mouse can be used in the "Base" mode to place the bases in the approximate position, though this is not required.
  3. The query fatm4 command can be used to set the correct geometry for the first hydrogen bond.
  4. To fix the remaining hydrogen bonded atom(s) rotate the base about the fourth atom from step 3 using the rotatm command.