Hi,
I've been loading Tinker's version of .xyz files into Jmol with unexpected
connections displayed.
Jmol writes a file with number of atoms followed by a blank line and a 4 column
atom format (symbol, x, y, z - 5 dec places).
17
C -0.55370 1.43900 -0.14471
C -0.46130 -0.00500 0.35261
C -1.75150 -0.74880 0.00170
C 0.72611 -0.69990 -0.31680
C 2.02730 -0.03280 0.13331
H -0.69280 1.44280 -1.22580
H -1.39970 1.93400 0.33220
H 0.36540 1.96880 0.10530
H -0.32230 -0.00880 1.43360
H -1.89060 -0.74500 -1.07940
H -1.68571 -1.77750 0.35590
H -2.59750 -0.25380 0.47851
H 0.73950 -1.75180 -0.03150
H 0.63160 -0.61830 -1.39960
H 2.01390 1.01910 -0.15200
H 2.12180 -0.11440 1.21610
H 2.87330 -0.52781 -0.34360
Tinker reads and writes additional information: some text in the first line (no
blank before atoms) and 6 columns (#, symbol, x, y, z - 6 dec places, FF type)
plus connection info for each atom.
17 spentane.xyz MM3 parameters
1 C -0.553700 1.439000 -0.144710 1 6 8 7 2
2 C -0.461300 -0.005000 0.352610 1 4 1 3 9
3 C -1.751500 -0.748800 0.001700 1 10 2 11 12
4 C 0.726110 -0.699900 -0.316800 1 14 13 5 2
5 C 2.027300 -0.032800 0.133310 1 17 4 15 16
6 H -0.692800 1.442800 -1.225800 5 1
7 H -1.399700 1.934000 0.332200 5 1
8 H 0.365400 1.968800 0.105300 5 1
9 H -0.322300 -0.008800 1.433600 5 2
10 H -1.890600 -0.745000 -1.079400 5 3
11 H -1.685710 -1.777500 0.355900 5 3
12 H -2.597500 -0.253800 0.478510 5 3
13 H 0.739500 -1.751800 -0.031500 5 4
14 H 0.631600 -0.618300 -1.399600 5 4
15 H 2.013900 1.019100 -0.152000 5 5
16 H 2.121800 -0.114400 1.216100 5 5
17 H 2.873300 -0.527810 -0.343600 5 5
In my observations, Jmol (14.0.1 applet) displays various incorrect connections
for the Tinker files, either bonding atoms that shouldn't be or not bonding
atoms that should be. The file listed above gives me one methyl group all
disconnected. What am I missing?
Thanks,
George Whitwell
NC Wesleyan College
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