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I have been conducting research on $\ce{C10}$ - $\ce{C16}$ alkanes and encountered an unusual error when I attempted to perform an optimization and frequency calculation on Tridecane at the G3 level of theory at 298 Kelvin. Additionally, Tridecane was the only molecule within the set to experience an error when run. I believe I have isolated my error to the Z-Matrix.

Input File:

%chk=TDG3
#N G3 Temperature=298 opt freq

opt freq calc Tridecane

0 1
C  
C     1    B1
C     2    B2   1    A1
C     3    B3   2    A2   1    D1
C     4    B4   3    A3   2    D2
C     5    B5   4    A4   3    D3
C     6    B6   5    A5   4    D4
C     7    B7   6    A6   5    D5
C     8    B8   7    A7   6    D6
C     9    B9   8    A8   7    D7
C    10   B10   9    A9   8    D8
C    11   B11  10   A10   9    D9
C    12   B12  11   A11  10   D10
H    13   B13  12   A12  11   D11
H    13   B14  12   A13  11   D12
H    13   B15  12   A14  11   D13
H    12   B16  11   A15  10   D14
H    12   B17  11   A16  10   D15
H    11   B18  10   A17   9   D16
H    11   B19  10   A18   9   D17
H    10   B20   9   A19   8   D18
H    10   B21   9   A20   8   D19
H     9   B22   8   A21   7   D20
H     9   B23   8   A22   7   D21
H     8   B24   7   A23   6   D22
H     8   B25   7   A24   6   D23
H     7   B26   6   A25   5   D24
H     7   B27   6   A26   5   D25
H     6   B28   5   A27   4   D26
H     6   B29   5   A28   4   D27
H     5   B30   4   A29   3   D28
H     5   B31   4   A30   3   D29
H     4   B32   3   A31   2   D30
H     4   B33   3   A32   2   D31
H     3   B34   2   A33   1   D32
H     3   B35   2   A34   1   D33
H     2   B36   1   A35   3   D34
H     2   B37   1   A36   3   D35
H     1   B38   2   A37   3   D36
H     1   B39   2   A38   3   D37
H     1   B40   2   A39   3   D38

B1  1.529941022
B2  1.529941022
B3  1.530022673
B4  1.529941022
B5  1.530022673
B6  1.529941022
B7  1.529941022
B8  1.530022673
B9  1.529941022
B10  1.530022673
B11  1.529941022
B12  1.529941022
B13  1.090066218
B14  1.090066218
B15  1.090008482
B16  1.090008482
B17  1.090008482
B18  1.090066218
B19  1.090066218
B20  1.090008482
B21  1.090008482
B22  1.090066218
B23  1.090066218
B24  1.090008482
B25  1.090008482
B26  1.090066218
B27  1.090066218
B28  1.090008482
B29  1.090008482
B30  1.090066218
B31  1.090066218
B32  1.090008482
B33  1.090008482
B34  1.090066218
B35  1.090066218
B36  1.090008482
B37  1.090008482
B38  1.090008482
B39  1.090066218
B40  1.090066218

A1  109.4723086
A2  109.4744707
A3  109.4744707
A4  109.4744707
A5  109.4744707
A6  109.4723086
A7  109.4744707
A8  109.4744707
A9  109.4744707
A10  109.4744707
A11  109.4723086
A12  109.4725572
A13  109.4725572
A14  109.4728391
A15  109.4704114
A16  109.4704114
A17  109.4714761
A18  109.4714761
A19  109.4704114
A20  109.4704114
A21  109.4714761
A22  109.4714761
A23  109.4704114
A24  109.4704114
A25  109.4725572
A26  109.4725572
A27  109.4693304
A28  109.4693304
A29  109.4725572
A30  109.4725572
A31  109.4693304
A32  109.4693304
A33  109.4725572
A34  109.4725572
A35  109.4704114
A36  109.4704114
A37  109.4728391
A38  109.4725572
A39  109.4725572

D1  180.0000000
D2  180.0000000
D3  180.0000000
D4  180.0000000
D5  180.0000000
D6  180.0000000
D7  180.0000000
D8  180.0000000
D9  180.0000000
D10  180.0000000
D11 -59.99687819
D12  59.99687819
D13  180.0000000
D14 -60.00082041
D15  60.00082041
D16 -59.99621620
D17  59.99621620
D18 -60.00082041
D19  60.00082041
D20 -59.99621620
D21  59.99621620
D22 -60.00082041
D23  60.00082041
D24 -59.99687819
D25  59.99687819
D26 -60.00015848
D27  60.00015848
D28 -59.99687819
D29  59.99687819
D30 -60.00015848
D31  60.00015848
D32 -59.99687819
D33  59.99687819
D34  119.9991796
D35 -119.9991796
D36  180.0000000
D37 -59.99687819
D38  59.99687819

Error:

Charge =  0 Multiplicity = 1
The name of the center is too long.
Authenticating with public key "imported-openssh-key"                                       
?
Error termination via Lnk1e in /cluster/software/gaussian/gaussian-09-
D.01/g09/l101.exe at Mon May  1 12:25:02 2017.
Job cpu time:       0 days  0 hours  0 minutes  0.1 seconds.
File lengths (MBytes):  RWF=      5 Int=      0 D2E=      0 Chk=      2 Scr=      
1

Not Solved; Work Around Established

I have not determined the source of the error; however, I have found a way to work around the cause of the error. By substituting a Cartesian Coordinate system for the Z-Matrix the error no longer occurs. This indicates the source of the error can be narrowed down to within the confines of the Z-Matrix.

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I once found this error when moving input files across computers. There break marks were present ^M but only visible in vi. I eliminated them with the usual procedure

:1,$s/^M//

and it worked. I didn't find the exact source of error either but that was the last time I found the error.

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  • 2
    $\begingroup$ The tool dos2unix does the same job, with a smaller overhead and possibly more reliable. Another possibility is to use a sed (on unix-like) command (see one-liners): sed 's/.$//'. In vim the abbreviation for 1,$ (first to last) is % (whole file). $\endgroup$ – Martin - マーチン Nov 15 at 21:25
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I'm not able to reproduce that error, but your input file also has another problem, which might be causing your problems but you should get a different error. Something along the line of:

Undefined symbol, bond length, card 14.

Undefined symbol, angle alpha, card 14.

Undefined symbol, bond length, card 15.

Undefined symbol, angle alpha, card 15.

Undefined symbol, angle beta, card 15

Undefined symbol, bond length, card 16.

Gaussian is very sensitive to wrong formating. Blank lines usually mean end of "block" so it doesn't find the variables/constants Ax and Dx. You need to remove those blank lines. After that I can open it with Gaussview and Gaussian09 has no problems starting it (did only some seconds to look if there's an input error).

That Z-Matrix also isn't very "clean", since there's no reason to define different variables/constants with the same value, one would be sufficient. For example B1 and B2, B4, B6, B7 and B9 are all the same, you can just use B1 for all of those which cleans up the whole Z-Matrix.

For example here 6 variables/constants are sufficient:

%chk=TDG3
#N G3 Temperature=298 opt freq

opt freq calc Tridecane

0 1
C  
C   1   R1          
C   2   R1           1   B1         
C   3   R1           2   B1          1   D1        
C   4   R1           3   B1          2   D1        
C   5   R1           4   B1          3   D1        
C   6   R1           5   B1          4   D1        
C   7   R1           6   B1          5   D1        
C   8   R1           7   B1          6   D1        
C   9   R1           8   B1          7   D1        
C   10  R1           9   B1          8   D1        
C   11  R1           10  B1          9   D1        
C   12  R1           11  B1          10  D1        
H   1   R2         2   A2        3   D1      
H   1   R2         2   A2        3   D2      
H   1   R2         2   A2        3   -D2    
H   2   R2         3   A2        4   -D2     
H   2   R2         3   A2        4   D2      
H   3   R2         4   A2        5   D2      
H   3   R2         4   A2        5   -D2     
H   4   R2         5   A2        6   -D2     
H   4   R2         5   A2        6   D2      
H   5   R2         6   A2        7   D2      
H   5   R2         6   A2        7   -D2     
H   6   R2         7   A2        8   -D2     
H   6   R2         7   A2        8   D2      
H   7   R2         8   A2        9   D2      
H   7   R2         8   A2        9   -D2     
H   8   R2         9   A2        10  -D2     
H   8   R2         9   A2        10  D2      
H   9   R2         10  A2        11  D2      
H   9   R2         10  A2        11  -D2     
H   10  R2         11  A2        12  -D2     
H   10  R2         11  A2        12  D2      
H   11  R2         12  A2        13  D2      
H   11  R2         12  A2        13  -D2     
H   12  R2         11  A2        10  D2      
H   12  R2         11  A2        10  -D2     
H   13  R2         12  A2        11  D1      
H   13  R2         12  A2        11  -D2     
H   13  R2         12  A2        11  D2      


R1 1.52996824
B1 109.47388108
D1 180.00000000
R2 1.09003735
A2 109.47134891
D2 59.99856213

But both your version(without the blank lines) and the one posted by me are running without problems for me.

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  • $\begingroup$ Do same bond lengths by one variable B1 for B2,4,6,7,9 mean that you force it to have symmetry? $\endgroup$ – pH13 - Yet another Philipp May 4 '17 at 12:30
  • $\begingroup$ @pH13-YetanotherPhilipp you mean that I force the length of all those bonds to be the same in the optimized structure? That's not the case. $\endgroup$ – DSVA May 4 '17 at 17:05
  • $\begingroup$ This is interesting! I always thought that If you are using the same variable, then only that variable gets optimised, but I guess you'll have to force g09 to not use redundant coordinates to achieve that. Just a side note: the supplied values in the z-matrix would be treated as constants (as they are read from the constants block). $\endgroup$ – Martin - マーチン Nov 15 at 21:37

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