Transition State Example

When you draw a structure in PCMODEL and save it in mopac format, PCMODEL writes a file with the atoms in a particular order, depending upon the bonding arrangement. The first atom listed is "atom 1", the second atom listed is "atom 2", etc. See the transition state example dat file. The line for each atom includes the following:

(atom type) (bond distance) (bond optimization flag)...
   (angle) (angle optimization flag)...
   (torsion angle) (torsion angle optimization flag)...
   (atom # to which this atom is bonded)...
   (atom # with which this atom makes an angle, 
      where the previous atom # is the angle vertex)...
   (atom # with which this atom makes a torsion angle,
       where the previous two atom #s are the vertices)...
   (partial charge). 

To calculate a transition state, the order of the atoms in the reactant and the product must be the same. However, the order in which PCMODEL lists the atoms in the mopac-style file MAY BE DIFFERENT for the reactant and product. To verify/change the order of the atoms so the reactant and product match:

1. Draw a diagram of your reactant. Include all hydrogens. Make the drawing very big.
2. Read through the reactant_product.dat file and label each atom on your reactant drawing with its atom number.
3. Draw a diagram of your product. Include all hydrogens. Make the drawing very big.
4. Label each atom on your product drawing with the SAME atom numbers used in the reactant drawing.
5. Edit the reactant_product.dat file so that the order of the product atoms corresponds with the atom numbers in the product drawing. Also edit the atom numbers on each line so that the bonding, angles, and torsion angles are still correct (this can be confusing---be careful!). Compare the transition state example dat file with mismatched order with the rearranged transition state example dat file.