We won't be able to read a "Tinker" file. It's not an "xyz" file. It's its
own format, and apparently it has no header with which to identify itself.
So if we do write a reader, it will never load these files directly. More
likely it would read them with a prefix such as:
load tinker::out.xyz
On Mon, Jan 20, 2014 at 2:31 PM, Whitwell, George <[email protected]>wrote:
> 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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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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