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I would like to generate a Z-matrix from the following XYZ file (C2H6dimer.xyz):

16
C2H6dimer
C    0.539202   -0.539202    1.933833
C   -0.539202    0.539202    1.933833
H    1.536064   -0.098299    1.932264
H    0.459532   -1.174264    2.816008
H    0.456405   -1.179449    1.055941
H   -1.536064    0.098299    1.932264
H   -0.459532    1.174264    2.816008
H   -0.456405    1.179449    1.055941
C    0.539202    0.539202   -1.933833
C   -0.539202   -0.539202   -1.933833
H    1.179449    0.456405   -1.055941
H    1.174264    0.459532   -2.816008
H    0.098299    1.536064   -1.932264
H   -1.174264   -0.459532   -2.816008
H   -0.098299   -1.536064   -1.932264
H   -1.179449   -0.456405   -1.055941

However I can't do it with the Gaussian utility called newzmat, because after typing newzmat -ixyz C2H6dimer.xyz -ozmat, I receive the following error message:

 Error in cartesian coordinates.
  WANTED A FLOATING POINT NUMBER AS INPUT.
  FOUND AN END-OF-LINE FOR INPUT.
 16
   ?
 Error termination via Lnk1e at Sun Jun 21 01:09:30 2020.
Segmentation fault

Could you please help me to figure out what the problem is?

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    $\begingroup$ Please include anything that is a prerequisite to create the problem. Am I right to assume that the program newzmat is a utility of Gaussian (which version)? $\endgroup$
    – Martin - マーチン ♦
    Commented Jun 21, 2020 at 0:46
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    $\begingroup$ Can you try to remove the last (empty) line? Gaussian can be very strict about empty lines in places it does not expect them. Maybe newzmat behaves similar. $\endgroup$
    – Feodoran
    Commented Jun 22, 2020 at 12:55

3 Answers 3

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According to the manual of the newzmat utility of Gaussian 16, it accepts unadorned Cartesian coordinates (G16 online manual). The format you have posted is actually (simple) xmol. This means the first line denotes the number of atoms, the second line denotes a comment, and both need to be skipped.

Therefore your file should look like this:

C    0.539202   -0.539202    1.933833
C   -0.539202    0.539202    1.933833
H    1.536064   -0.098299    1.932264
H    0.459532   -1.174264    2.816008
H    0.456405   -1.179449    1.055941
H   -1.536064    0.098299    1.932264
H   -0.459532    1.174264    2.816008
H   -0.456405    1.179449    1.055941
C    0.539202    0.539202   -1.933833
C   -0.539202   -0.539202   -1.933833
H    1.179449    0.456405   -1.055941
H    1.174264    0.459532   -2.816008
H    0.098299    1.536064   -1.932264
H   -1.174264   -0.459532   -2.816008
H   -0.098299   -1.536064   -1.932264
H   -1.179449   -0.456405   -1.055941

In Gaussian terms, a block of cartesian coordinates is also a z-matrix. Therefore you also need to tell Gaussian to rebuild it (-rebuildzmat). This will likely fail on your input with an error:

Input z-matrix variables are not compatible with final structure.

If you allow rounding (-round) it will work. The complete command is:

newzmat -ixyz -ozmat -round -rebuildzmat <input.xyz> <output.com>

The following file is produced (it is a valid Gaussian input file):

# HF/6-31G* Test

-- No Title Specified --

 0,1
 C
 C,1,R2
 H,1,R3,2,A3
 H,1,R4,2,A4,3,D4,0
 H,1,R5,2,A5,3,D5,0
 H,2,R6,1,A6,3,D6,0
 H,2,R7,1,A7,6,D7,0
 H,2,R8,1,A8,6,D8,0
 C,3,R9,1,A9,2,D9,0
 C,9,R10,3,A10,1,D10,0
 H,9,R11,3,A11,10,D11,0
 H,9,R12,3,A12,10,D12,0
 H,9,R13,3,A13,10,D13,0
 H,10,R14,9,A14,3,D14,0
 H,10,R15,9,A15,14,D15,0
 H,10,R16,9,A16,14,D16,0
      Variables:
 R2=1.53
 R3=1.09
 R4=1.09
 R5=1.09
 R6=1.09
 R7=1.09
 R8=1.09
 R9=4.04
 R10=1.53
 R11=1.09
 R12=1.09
 R13=1.09
 R14=1.09
 R15=1.09
 R16=1.09
 A3=111.
 A4=111.
 A5=111.
 A6=111.
 A7=111.
 A8=111.
 A9=81.
 A10=94.
 A11=22.
 A12=128.
 A13=104.
 A14=111.
 A15=111.
 A16=111.
 D4=120.
 D5=-120.
 D6=180.
 D7=120.
 D8=-120.
 D9=-76.
 D10=-21.
 D11=-144.
 D12=-120.
 D13=113.
 D14=167.
 D15=120.
 D16=-120.

 1 2 1.000 3 1.000 4 1.000 5 1.000
 2 1 1.000 6 1.000 7 1.000 8 1.000
 3 1 1.000
 4 1 1.000
 5 1 1.000
 6 2 1.000
 7 2 1.000
 8 2 1.000
 9 10 1.000 11 1.000 12 1.000 13 1.000
 10 9 1.000 14 1.000 15 1.000 16 1.000
 11 9 1.000
 12 9 1.000
 13 9 1.000
 14 10 1.000
 15 10 1.000
 16 10 1.000

Whether or not this z-matrix does actually fits the purpose you are needing it for, is a different question. For the most tasks, where z-matrices are the superior input, I recommend building it by hand.

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I copied and pasted your XYZ into this and got the Z-matrix for your XYZ coordiantes (see below). Geoff Hutchison's comment points out that this uses OpenBabel. Here is a ZMAT for your XYZ coordinates:

16
C   1
C   1 1.525
H   1 1.090  2 111.141
H   1 1.090  2 111.120  3 119.9
H   1 1.090  2 111.206  3 239.9
H   2 1.090  1 111.141  3 179.8
H   2 1.090  1 111.120  3 299.7
H   2 1.090  1 111.206  3  59.7
C   8 3.216  2 130.964  1  32.0
C   9 1.525  8  85.518  2  56.3
H   9 1.090  8  56.495  2 297.1
H   9 1.090  8 161.358  2 262.3
H   9 1.090  8  72.021  2 170.2
H  10 1.090  9 111.120  8 129.0
H  10 1.090  9 111.141  8 248.9
H  10 1.090  9 111.206  8   9.1

In my experience, this is the fastest and easiest way to to convert an XYZ file to Z-matrix format, except maybe in extremely difficult cases.

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    $\begingroup$ Incidentally, this uses Open Babel behind the scenes. $\endgroup$
    – Geoff Hutchison
    Commented Oct 14, 2022 at 14:05
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There is a way to do this in Avogadro Molecular Editor and Visualizer that you can download freely.

  1. Open your .xyz file in Avogadro. Click on the extensions in the top.

  2. In the extensions, select Gaussian. This opens a guassian input editor like below.

  3. Change the format to Z-matrix or Z-matrix (compact), whichever one you like.

This editor has a nice interface that you can use to edit your Gaussian input.

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    $\begingroup$ Incidentally, this also uses Open Babel behind the scenes. $\endgroup$
    – Geoff Hutchison
    Commented Dec 30, 2022 at 0:55

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