Hello Bob and Jmol community,
I would like to report a (minor) bug related to the original topic of this
post.
If one uses the model kit to add, let's say, a double bond to a molecule,
the reported
data from a UFF minimization will show the wrong number of atoms.
For instance, using benzene as a test case, adding 3 doubles to the ring and
performing a minimization (with zero steps) will result in :
logLevel = 6
Initial E = 337.322 kJ/mol criterion = 0.001000 max steps = 0
Universal Force Field -- Rappe, A. K., et. al.; J. Am. Chem. Soc. (1992)
114(25) p. 10024-10035
Jmol Minimization Version 12.1.51_dev 2011-06-29 11:15
S T E E P E S T D E S C E N T
ATOM X Y Z TYPE GRADX GRADY GRADZ
---------BONDED ATOMS--------
-----------------------------------------------------------------------------------------------
1 3.885 17.722 24.599 C_R 0.000 0.000 0.000 2 6
17
2 3.499 18.381 25.768 C_R 0.000 0.000 0.000 1 3
15
3 2.560 19.410 25.710 C_R 0.000 0.000 0.000 2 4
16
4 1.986 19.767 24.490 C_R 0.000 0.000 0.000 3 5
13
5 2.363 19.102 23.319 C_R 0.000 0.000 0.000 4 6
14
6 3.300 18.061 23.365 C_R 0.000 0.000 0.000 1 5
7
7 3.703 17.403 22.103 H_ 0.000 0.000 0.000 6
13 1.237 20.571 24.449 H_ 0.000 0.000 0.000 4
14 1.921 19.398 22.356 H_ 0.000 0.000 0.000 5
15 3.936 18.088 26.734 H_ 0.000 0.000 0.000 2
16 2.271 19.942 26.629 H_ 0.000 0.000 0.000 3
17 4.651 16.933 24.643 H_ 0.000 0.000 0.000 1
Apparently, changing a bond affects the total number of atoms.
Unfortunately, this bug is also being propagated into the reported bond,
angle, torsion, out-of-plane data of the log data as well.
Jen
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