Re: [Jmol-developers] internal coordinates?

Bob Hanson Tue, 01 Jun 2004 12:14:42 -0700

Miguel, all you do is read these data in and immediately convert to cartesian coordinates. It's set up so that you stream the data in. The first three points are unique, because:

a) The first point (#1) is automatically just at position 0,0,0. b) The second point (#2) is a given distance from that point, #NA=1 along X c) The third point (#3) is a given distance from atom #NA=2 with a given angle in the xy plane for NA-NB-#3. d) All additional points (#X) are referenced to previous points by indicating a distance from a previous point (NA-#X), an angle back to two points (NA-NB-#X), and a torsional angle back to three previous points (NA-NB-NC-#X)

see http://www.cmbi.kun.nl/tutorials/cheminf/mopac/intc.html
for a nice description of a "z-matrix"

Bob


Miguel wrote:

internal coordinates SHOULD be very easy to use, particularly if they are
handed
to you and you don't have to generate them yourself. They are amazingly
concise.

We are already handling fractional coordinates, so adding another
coordinate system will not be difficult ... IF ...

The only complication I can imagine is that they sometimes involve
"phantom" or
"temporary" atoms for starting points.

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

... IF ... there are three floats per atom.

Q: Is it the case that there are only 3 numbers per atom? bondLength,
BondAngle, and TorsonAngle?

Q: What are NA, NB, and NC?

Miguel

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--

Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr

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Re: [Jmol-developers] internal coordinates?

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