Appendix 1-Adding a base

To use builder you need:

• coordinates of the ring atoms.
• United atom atomic weights for the ring(and some off ring in the case of pyrimidines)
• Connectivity in pdb format.
• NAMOT2 supports vdw contact calculations. To accommodate this, NAMOT2 needs to know the atom characteristics. A file with the indices to the atom type is required.

  The indices:

    Atom type      R   Index
     c         1.850   1
     c2        1.925   2
     c3        2.000   3
     o         1.600   4
     os        1.650   5
     n         1.750   6
     p         2.100   7
     h         1.000   8
  

• For any atoms that you wish to add that aren't in the crd file, bond length, angle, and torsional angle, is needed.
• In the case of a non-standard purine/pyrmidine ring system(or more likely a different ribose connection) more information is needed.
  • Sign of the N1-C2-N3 cross product when the alpha face is up. (positive for purines, negative for pyrimidines).
  • Atoms used to determine the orientation("1 2 3 9" for purines, "1 2 3 1" for pyrimidines. The first three are almost always going to be "1 2 3" this represents N1,C2,N3. These are used in determination of alpha face direction. The fourth bit of information is the base atom that is connected to C1'.
  • The two base atoms on either side of the atom connected to the ribose. These are used to determine the position of C1*.