How to do it faster

Start SYBYL, Build/Edit menu, Get fragment, select 2-norbornene.
Under Compute, Interfaces, MOPAC, change the default setting to Optimization/Full and enter a name (nbn in the example); then Submit.
Very soon the 'job completed' message will appear in the Sybyl command window, and nine files with the name 'nbn' will be produced.
The .sta file is what MOPAC itself calls the .arc file. We continue with this file.

We can extract a new input file with z-matrix with the tail command:

tail -21 nbn.sta >nbnts.dat
In the SYBYL fragment 2-norbornene the numbering is such that both bonds appear in the z-matrix, so no editting is required. The symmetry and reaction path can be added directly. The correct file will look like this:
 AM1 T=3600 SYMMETRY
 ~nbnts.dat
 
  C    0.0000000  0      0.000000  0      0.000000  0    0    0    0     -0.0977
  C    1.5230894  1      0.000000  0      0.000000  0    1    0    0     -0.1741
  C    1.3532585  1    107.669299  1      0.000000  0    2    1    0     -0.1741
  C    1.5238184  1    107.816982  1     -1.052910  1    3    2    1     -0.0977
  C    1.5500802 -1    105.674136  1    -68.763017  1    4    3    2     -0.1576
  C    1.5503404  0    105.408439  1     70.402362  1    1    2    3     -0.1579
  C    1.5643220  1     99.447895  1     34.615269  1    4    3    2     -0.1597
  H    1.1032318  1    116.457146  1   -160.066070  1    1    2    3      0.1115
  H    1.0867650  1    122.863604  1   -179.460005  1    2    1    3      0.1408
  H    1.0869154  1    129.346081  1   -179.282694  1    3    2    1      0.1403
  H    1.1027851  1    116.562781  1    161.488555  1    4    3    2      0.1115
  H    1.1140700  1    111.138396  1    -53.299588  1    5    4    3      0.0860
  H    1.1153358  1    110.408520  1   -173.921421  1    5    4    3      0.0819
  H    1.1157912  1    110.290331  1    174.371210  1    6    1    2      0.0815
  H    1.1142537  1    111.284518  1     53.778678  1    6    1    2      0.0863
  H    1.1101529  1    112.943218  1     65.992931  1    7    4    3      0.0918
  H    1.1101056  1    113.101074  1   -168.027364  1    7    4    3      0.0874

 5  1  6

 1.6  1.7  1.8  1.9  2.0  2.1  2.2  2.3  2.4  2.5  3.0  4.0

As remarked before, the command mode in SYBYL allows for the set-up of a z-matrix, introduction of a reaction coordinate, etc. So probably it can be done even faster after investing some time in studying the manual.


Back to Exercise.