For example, in this example we have a first atom at 0,0,0, then two phantom atoms on roughly perpendicular axes. They define the starting point for the next dihedral, and you are off and running. Mostly QM programs start with these so as to define positions when symmetry is an issue.
ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE
NUMBER SYMBOL (ANGSTROMS) (DEGREES) (DEGREES)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 C( 1) 0.000000 0.000000 0.000000
2 XX( ) 4.117293 0.000000 0.000000 1
3 XX( ) 2.303156 90.000000 0.000000 2 1
4 C( 2) 1.351924 * 133.488008 * 180.000000 * 1 2 3
5 C( 3) 1.540002 * 119.999966 * 0.000000 * 4 1 2
6 C( 4) 1.351924 * 119.999976 * 0.000000 * 5 4 1
7 C( 5) 1.540000 * 119.999984 * 0.000000 * 6 5 4
8 C( 6) 1.351923 * 120.000040 * 0.000000 * 7 6 5
9 C( 7) 1.540000 * 119.999988 * 180.000000 * 8 7 6
10 H( 8) 1.090000 * 106.512015 * 180.000000 * 1 2 4
11 H( 9) 1.090000 * 119.999974 * 180.000000 * 4 1 5
12 H( 10) 1.090000 * 120.000036 * 180.000000 * 5 4 6
13 H( 11) 1.089999 * 119.999979 * 180.000000 * 6 5 7
14 H( 12) 1.090000 * 119.999963 * 180.000000 * 7 6 8
15 H( 13) 1.090000 * 119.999999 * 180.000000 * 9 8 7
16 H( 14) 1.089999 * 120.000004 * 180.000000 * 9 8 15
E.L. Willighagen wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
On Tuesday 01 June 2004 16:03, Miguel wrote:
Note that there are several options for MOPAC output files. "xyz coordinates" is one of them. Are you reading the internal coord or the xyz coord?
Someone here in Spain asked me about internal coordinates this morning.
Q: Is it important? Or just a nice-to-have?
Internal coordinates are very often used for input for quantum mechanical programs... and can also often be found in the output again.
Egon
- -- [EMAIL PROTECTED]
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6
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