Feature Requests item #871696, was opened at 2004-01-06 08:47
Message generated for change (Settings changed) made by hansonr
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Category: New IO Format
Group: None
Status: Open
Priority: 5
Submitted By: Egon Willighagen (egonw)
>Assigned to: Egon Willighagen (egonw)
Summary: A Z-matrix Guassian input file Reader
Initial Comment:
See CDK RFE #871694.
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Comment By: Miguel (migueljmol)
Date: 2004-10-14 16:19
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The 'variable's and 'constants' do not look overly
complicated to me.
But, if we are going to do this then I need more specific
direction on *exactly* what to do. And it will need to wait
at least until mid-November 2004.
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Comment By: Rene Kanters (rkanters)
Date: 2004-10-13 06:45
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Actually z-matrices in Gaussian input (or some other programs for that
matter) can be a bit trickier in that they may have variables and
constants in their definitions, e.g.,
X
X 1 rx
C 2 rc 1 a90
C 2 rc 1 a90 3 t180
H 2 rh1 1 a1 3 t0
H 2 rh2 1 a2 3 t180
H 2 xh 3 a3 1 t180
Br 2 xbr 3 a4 1 t180
variables
rc 0.60002733
rh1 1.66512683
rh2 1.66512683
a1 89.62647357
a2 89.62647357
xh 2.47262334
xbr 3.90355994
a3 90.0
a4 90.0
constants
rx 1.0
a90 90.0
t180 180.
t0 0.
which makes interpreting a bit trickier (they actually also can have
things like -a3 in them...).
I would suggest, since the question was about Gaussian input files, to use
Gaussians newzmat tool to convert the input z-matrix to something like
an xyz file, with the format:
newzmat -izmat infputfilename.com -oxyz outputfilename.xyz
The only thing is that you will loose your dummy atoms, since Gaussian
strips those from its cartesian output (both in regular output and in
newzmat output).
I hope this helps.
Ren�
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Comment By: Miguel (migueljmol)
Date: 2004-09-29 09:57
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OK, I have a basic understanding of internal coordinates.
But I thought that you started off with a couple of real points
(and perhaps an artificial point) and went from there. I do not
understand anything about the Z-matrix representation.
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Comment By: Nobody/Anonymous (nobody)
Date: 2004-09-28 08:31
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z-matrix means internal coordinate used by the mopac or the
gamess etc.
------
C
O 1 1.2000
H 1 1.1000 2 120.0000
C 1 1.5000 2 120.0000 3 180
H 4 1.1000 1 110.0000 2 0
H 4 1.1000 1 109.9999 2 -120.0000
H 4 1.1000 1 109.9999 2 120
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Comment By: Miguel (migueljmol)
Date: 2004-05-26 03:21
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Egon,
Is this done?
I am not sure what you mean by 'Z-matrix'
Miguel
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