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Converting a molecular z-matrix output from DASH into Topas format
lksbath #1
User title: Lucy Saunders
Member since Jul 2015 · 21 posts · Location: University of Bath/Diamond Light Source
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Subject: Converting a molecular z-matrix output from DASH into Topas format
Hi all,

Has anyone ever taken a z-matrix for a molecule from DASH and converted it into Topas format? I have had a go at doing this but the z-matrix scrambles up my molecule. I used the oxa inp file in tutorial 24 on the Durham community page as a basis for generated my own z-matrix.

Here is a line from my dash z-matrix:
C      1.4055394  0   132.409002  0   179.661007  0    1    2    3  3.0  1.0   11 C12 C13 N4 C8

and here is how how I have input that line into topas:
load  z_matrix {
C12 C13 c12c13 1.4055394 N4 c12c13n4     132.409002 C8 c12c13c8n4 179.661007
}

Can anyone spot the error?

Thanks
AlanCoelho #2
Member since Aug 2011 · 294 posts
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You have got:

load  z_matrix {
    C12
    C13 c12c13 1.4055394
    N4 c12c13n4     132.409002
    C8 c12c13c8n4 179.661007
}

Z-matrix should have one atom on the first line. Two on the second, three on the third and four onwards. In your description you have one atom on each line. My guess is that you want to write some space there. Topas uses the standard Z-matrix format except parameters can have names or equations. Best to have a look at z-matrix format; try https://en.wikipedia.org/wiki/Z-matrix_%28chemistry%29
lksbath #3
User title: Lucy Saunders
Member since Jul 2015 · 21 posts · Location: University of Bath/Diamond Light Source
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Thanks for your reply Alan. That was just one line from my matrix. Here is the start of it, I think this agrees more with what you were saying (I should have put this on my post to start to be more clear, sorry):

load z_matrix {
C13
N4 C13 c13n4 1.3772045
C8 C13 c13c8 1.3994884 N4 c8c13n4 106.142410
C12 C13 c12c13 1.4055394 N4 c12c13n4 132.409002 C8 c12c13n4c8 179.661007
H100 N4 h100n4 0.9306757 C13 h100n4c13 131.404716 C8 h100n4c13c8 -177.101612
C14 N4 c14n4 1.3475339 C13 c14n4c13 107.00147 H100 c14n4c13h100 175.530630
...
}

This format, however, scrambles my molecule.

Here is the corresponding DASH output for the lines above:
1.0 1.0 1.0 90.0 90.0 90.0
  15   0
  C      0.0000000  0     0.000000  0     0.000000  0    0    0    0  3.0  1.0   10 C13
  N      1.3772045  0     0.000000  0     0.000000  0    1    0    0  3.0  1.0    7 N4 C13
  C      1.3994884  0   106.142410  0     0.000000  0    1    2    0  3.0  1.0    9 C8 C13 N4
  C      1.4055394  0   132.409002  0   179.661007  0    1    2    3  3.0  1.0   11 C12 C13 N4 C8
  H      0.9306757  0   131.404716  0  -177.101612  0    2    1    3  6.0  1.0    5 H100 N4 C13 C8
  C      1.3475339  0   107.001447  0   175.530630  0    2    1    5  3.0  1.0   14 C14 N4 C13 H100
AlanCoelho #4
Member since Aug 2011 · 294 posts
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I copied your rigid fragment to the rigid body editor and got the display in the attached. Is this what you expect.
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lksbath #5
User title: Lucy Saunders
Member since Jul 2015 · 21 posts · Location: University of Bath/Diamond Light Source
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Hi Alan,

Yes! That fragment is what I expect. Attached is a picture of the whole molecule. I have just used the New Rigid Body editor to check all my z-matrices and they give the structures I am expecting. It is definitely a case that my coordinates and z-matrix are not matching up so I think it is definitely the placement of my fragment. Do you know how I can sort this?

Thanks!

Lucy
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This post was edited on 2015-07-27, 11:53 by lksbath.
lksbath #6
User title: Lucy Saunders
Member since Jul 2015 · 21 posts · Location: University of Bath/Diamond Light Source
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Problem sorted!
This post was edited 2 times, last on 2015-08-05, 14:29 by lksbath.
johnsoevans (Administrator) #7
User title: John Evans
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Just so the link is on the same page as this thread, see also: https://github.com/mspillman/zmatrix-to-inp
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