# Unix/MobaXterm Project Assistence (Knowing the Error in my Output File)

I'm a student and I recieved a project in which I am supposed to simulate a transition state in an $\mathrm{S_N2}$ reaction.

The first instruction in this project is to use a benchmark reaction in order to establish the best level of theory. The reaction is $\mathrm{S_N2}$ with the following reactants: $\ce{MeCH2Cl + Cl-}$ and with the following level of theory: HF/6-31+G(d,p).

In summary this is what I did:

1. I used Gaussview to create the reactants (in the same file) and the transition state.
2. I saved the files and moved them to Mobaxterm for editing the text and setting the level of theory.
3. I condensed all the data into one input file and used the Opt = QST3 method for simulating the transition state.

I recieved the error:

Constants:
Undefined symbol, angle beta, card   9.
Error termination via Lnk1e in /private/chem/g09E01/g09/l101.exe at Sat Aug  5 09:07:08 2017.
Job cpu time:       0 days  0 hours  0 minutes  0.9 seconds.
File lengths (MBytes):  RWF=      5 Int=      0 D2E=      0 Chk=      3 Scr=      1
Error: segmentation violation


Here is my input file:

%chk=Reactants.chk
%mem=4000MB
%nproc=4
#P opt HF/6-31+G(d,p) Opt=QST3

MeCH2Cl (Chloroethane) + Cl^-

0 1
C
H                  1            B1
H                  1            B2    2            A1
C                  1            B3    3            A2    2            D1    0
H                  4            B4    1            A3    3            D2    0
H                  4            B5    1            A4    3            D3    0
H                  4            B6    1            A5    3            D4    0
Cl                 1            B7    4            A6    7            D5    0
Cl                 1            B8    4            A7    7            D6    0

B1             1.07000000
B2             1.07000000
B3             1.54000000
B4             1.07000000
B5             1.07000000
B6             1.07000000
B7             1.76000000
B8             2.00000000
A1           109.47122063
A2           109.47122063
A3           109.47122063
A4           109.47122063
A5           109.47122063
A6           109.47122063
A7           115.75316236
D1           120.00000000
D2          -180.00000000
D3           -60.00000000
D4            60.00000000
D5           -60.00000000
D6           120.46043739

Product MeCH2Cl + Cl^-

0 1
C
H                  1            B1
H                  1            B2    2            A1
C                  1            B3    3            A2    2            D1    0
H                  4            B4    1            A3    3            D2    0
H                  4            B5    1            A4    3            D3    0
H                  4            B6    1            A5    3            D4    0
Cl                 1            B7    4            A6    7            D5    0
Cl                 1            B8    4            A7    7            D6    0

B1             1.07000000
B2             1.07000000
B3             1.54000000
B4             1.07000000
B5             1.07000000
B6             1.07000000
B7             1.76000000
B8             2.00000000
A1           109.47122063
A2           109.47122063
A3           109.47122063
A4           109.47122063
A5           109.47122063
A6           109.47122063
A7           115.75316236
D1           120.00000000
D2          -180.00000000
D3           -60.00000000
D4            60.00000000
D5           -60.00000000
D6           120.46043739

TS MeCH2Cl2

0 2
C
H                  1            E1
H                  1            E2    2            F1
C                  1            E3    3            F2    2            G1    0
H                  4            E4    1            F3    3            G2    0
H                  4            E5    1            F4    3            G3    0
H                  4            E6    1            F5    3            G4    0
Cl                 1            E7    4            F6    7            G5    0
Cl                 1            E8    4            F7    7            G6    0

E1             1.06999987
E2             1.06999978
E3             1.54000000
E4             1.07000000
E5             1.07000000
E6             1.07000000
E7             2.20000000
E8             2.20000000
F1           120.00007951
F2           119.99972580
F3           109.47120255
F4           109.47120255
F5           109.47123134
F6            90.00004829
F7            90.00004855
G1           180.00000000
G2            59.99830388
G3           179.99831867
G4           -60.00168873
G5            29.99845985
G6          -150.00183223


I also don't know how to format the input file text in a way that it will keep its original form. Thanks for the help. Any guidance would mean a lot to me.

• For code I'd use ... (backquote symbol, typically located on a tilde (~) key), also check out How can I format math/chemistry expressions here? – andselisk Aug 5 '17 at 6:39
• "I saved the files and moved them to Mobaxterm for editing the text and setting the level of theory." What do you mean? How did you move them to MobaXTerm (do you know what MobaXterm is?) and why didn't you just set the correct input paramaters in the first place? This problem clearly doesn't have anything to do with MobaXterm or Unix... – DSVA Aug 5 '17 at 9:22
• The method I learned in class was to first build the molecule in GaussView, after that save the file in my desktop (as .jgf). Then I would drag it into MobaxTerm and edit the text there. – H B Aug 7 '17 at 11:32

I already tested the TS search calculation of this reaction based on your proposed structure coordinates. The calculation has been terminated quickly at link9999.exe sub-routine program in which its error message being implies that your initial geometry coordinate is not good enough for TS search by using QST3 method.

When you deal with QST3 you have to carefully consider whether your initial guess structure for Reactant, Product, and TS are consistent or not. I did adjust the position of some atoms and their order. As you see the figure below, the Cl atoms (number 8 & 9) which are opposite side have the similar bond distance for TS structure. Also note that better guess structure, better optimized structure (garbage in, garbage out).

By the way, the number of electron and charge and spin multiplicity that you set are not correct. Since there is Cl anion they should be 52, -1, and 1, respectively.

Here is your fixed gaussian input

%chk=TS-OPT-QST3-HF.chk
%mem=1000MB
%nprocshared=2
#p opt=qst3 freq hf/6-31+g(d,p) gfinput

MeCH2Cl (Chloroethane) + Cl^-

-1 1
C                  0.00000000    0.00000000    0.00000000
H                  0.00000000    0.00000000    1.07000000
H                  1.00880567    0.00000000   -0.35666667
C                 -0.72596296    1.25740473   -0.51333333
H                 -1.73476864    1.25740473   -0.15666667
H                 -0.22156012    2.13105608   -0.15666667
H                 -0.72596296    1.25740473   -1.58333333
Cl                -0.82967196   -1.43703398   -0.58666667
Cl                 1.87443357    0.38660782    1.34616685

Product MeCH2Cl + Cl^-

-1 1
C                  0.05335154    0.01100392    0.03831562
H                 -0.62960365   -0.59030929    0.60124957
H                  0.25817241   -0.64302643   -0.78338549
C                 -0.67261142    1.26840866   -0.47501772
H                 -1.68141709    1.26840866   -0.11835105
H                 -0.16820858    2.14206000   -0.11835105
H                 -0.67261142    1.26840866   -1.54501772
Cl                -1.06646990   -1.92858370   -0.75351772
Cl                 1.44289489    0.29760161    1.03624759

TS MeCH2Cl2

-1 1
C                  0.00002466    0.00041433   -0.00004215
H                  0.37333169   -0.90857336    0.42337605
H                  0.56365981    0.90508352    0.09370541
C                 -1.33365185    0.00041433   -0.77004668
H                 -1.39031750   -0.87322218   -1.38522816
H                 -2.14693922    0.00038473   -0.07473118
H                 -1.39034379    0.87408048   -1.38518364
Cl                 1.01053970   -0.23517338   -1.75028838
Cl                -1.01018689    0.24110207    1.74968530


I also strongly suggest you to add Freq keyword to invoke the program to print out you the vibrational mode and frequencies values for confirming later if the last optimized TS searched is the desired TS.

• "Also note that better guess structure, better optimized structure (garbage in, garbage out)." not necessarily, once you are close enough the result will be the same. It takes longer if you are further away but that's it. – DSVA Aug 5 '17 at 9:32
• Thanks. How in the first place do I determine the best guess structure? It seems like I'm more likely to get it wrong. – H B Aug 7 '17 at 11:35
• I tried running your inpout file but I recieved this error message in the output: Symbolic Z-matrix: Charge = -1 Multiplicity = 1 (had to delete coordinates) End of file in ZSymb. Error termination via Lnk1e in /private/chem/g09E01/g09/l101.exe at Mon Aug 7 15:02:53 2017. Job cpu time: 0 days 0 hours 0 minutes 0.3 seconds. File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 2 Scr= 1 Error: segmentation violation – H B Aug 7 '17 at 12:05
• @HB It's hard to fix the issue without seeing the complete input or output file. Can you please upload to a public website (e.g. pastebin.com). I would be happy to help you. – rangsiman Aug 8 '17 at 6:24
• I very, very strongly discourage compound jobs with Gaussian (adding the freq keyword). If anything fails in the second part, it compromises your checkpoint file which might not be recoverable. You can always read in the results of a completed calculation, but if something fails you might carry on a mistake and don't even realise it. – Martin - マーチン Sep 7 '17 at 10:11

I copied your input into a new file, added some empty lines at the end and changed the input line to be "#p opt=qst3 hf/6-31..." instead of redundant (and maybe erroneous(?) "opt ... opt=qst3"). I dropped the memory and processor line, as I defined some defaults in the Default.Route file. Using the following input, the calculation runs smoothly towards a transition state.

%chk=Reactants.chk
#P opt=qst3 HF/6-31+G(d,p)

MeCH2Cl (Chloroethane) + Cl^-

0 1
C
H                  1            B1
H                  1            B2    2            A1
C                  1            B3    3            A2    2            D1    0
H                  4            B4    1            A3    3            D2    0
H                  4            B5    1            A4    3            D3    0
H                  4            B6    1            A5    3            D4    0
Cl                 1            B7    4            A6    7            D5    0
Cl                 1            B8    4            A7    7            D6    0

B1             1.07000000
B2             1.07000000
B3             1.54000000
B4             1.07000000
B5             1.07000000
B6             1.07000000
B7             1.76000000
B8             2.00000000
A1           109.47122063
A2           109.47122063
A3           109.47122063
A4           109.47122063
A5           109.47122063
A6           109.47122063
A7           115.75316236
D1           120.00000000
D2          -180.00000000
D3           -60.00000000
D4            60.00000000
D5           -60.00000000
D6           120.46043739

Product MeCH2Cl + Cl^-

0 1
C
H                  1            B1
H                  1            B2    2            A1
C                  1            B3    3            A2    2            D1    0
H                  4            B4    1            A3    3            D2    0
H                  4            B5    1            A4    3            D3    0
H                  4            B6    1            A5    3            D4    0
Cl                 1            B7    4            A6    7            D5    0
Cl                 1            B8    4            A7    7            D6    0

B1             1.07000000
B2             1.07000000
B3             1.54000000
B4             1.07000000
B5             1.07000000
B6             1.07000000
B7             1.76000000
B8             2.00000000
A1           109.47122063
A2           109.47122063
A3           109.47122063
A4           109.47122063
A5           109.47122063
A6           109.47122063
A7           115.75316236
D1           120.00000000
D2          -180.00000000
D3           -60.00000000
D4            60.00000000
D5           -60.00000000
D6           120.46043739

TS MeCH2Cl2

0 2
C
H                  1            E1
H                  1            E2    2            F1
C                  1            E3    3            F2    2            G1    0
H                  4            E4    1            F3    3            G2    0
H                  4            E5    1            F4    3            G3    0
H                  4            E6    1            F5    3            G4    0
Cl                 1            E7    4            F6    7            G5    0
Cl                 1            E8    4            F7    7            G6    0

E1             1.06999987
E2             1.06999978
E3             1.54000000
E4             1.07000000
E5             1.07000000
E6             1.07000000
E7             2.20000000
E8             2.20000000
F1           120.00007951
F2           119.99972580
F3           109.47120255
F4           109.47120255
F5           109.47123134
F6            90.00004829
F7            90.00004855
G1           180.00000000
G2            59.99830388
G3           179.99831867
G4           -60.00168873
G5            29.99845985
G6          -150.00183223
<- blank line
<- blank line
<- blank line
<- blank line


The result is a transition state with one imaginary frequency at $-823.9116~\mathrm{cm^{-1}}$.

Then I realized the Charge and Multiplicity as was also criticized by rangsiman. So your slightly modified input works for me, but the result is a transition state for "charge=0 multiplicity=2" instead of "charge=-1 and multiplicity=1".

The optimization for the correct charge/multiplicity took roughly 4 minutes on my computer and the corresponding frequency calculation took 35 seconds. The result is a transition state with an imaginary frequency at $-363.5245~\mathrm{cm⁻1}$.

%chk=Reactants.chk
#P opt=qst3 HF/6-31+G(d,p)

MeCH2Cl (Chloroethane) + Cl^-

-1 1
C
H                  1            B1
H                  1            B2    2            A1
C                  1            B3    3            A2    2            D1    0
H                  4            B4    1            A3    3            D2    0
H                  4            B5    1            A4    3            D3    0
H                  4            B6    1            A5    3            D4    0
Cl                 1            B7    4            A6    7            D5    0
Cl                 1            B8    4            A7    7            D6    0

B1             1.07000000
B2             1.07000000
B3             1.54000000
B4             1.07000000
B5             1.07000000
B6             1.07000000
B7             1.76000000
B8             2.00000000
A1           109.47122063
A2           109.47122063
A3           109.47122063
A4           109.47122063
A5           109.47122063
A6           109.47122063
A7           115.75316236
D1           120.00000000
D2          -180.00000000
D3           -60.00000000
D4            60.00000000
D5           -60.00000000
D6           120.46043739

Product MeCH2Cl + Cl^-

-1 1
C
H                  1            B1
H                  1            B2    2            A1
C                  1            B3    3            A2    2            D1    0
H                  4            B4    1            A3    3            D2    0
H                  4            B5    1            A4    3            D3    0
H                  4            B6    1            A5    3            D4    0
Cl                 1            B7    4            A6    7            D5    0
Cl                 1            B8    4            A7    7            D6    0

B1             1.07000000
B2             1.07000000
B3             1.54000000
B4             1.07000000
B5             1.07000000
B6             1.07000000
B7             1.76000000
B8             2.00000000
A1           109.47122063
A2           109.47122063
A3           109.47122063
A4           109.47122063
A5           109.47122063
A6           109.47122063
A7           115.75316236
D1           120.00000000
D2          -180.00000000
D3           -60.00000000
D4            60.00000000
D5           -60.00000000
D6           120.46043739

TS MeCH2Cl2

-1 1
C
H                  1            E1
H                  1            E2    2            F1
C                  1            E3    3            F2    2            G1    0
H                  4            E4    1            F3    3            G2    0
H                  4            E5    1            F4    3            G3    0
H                  4            E6    1            F5    3            G4    0
Cl                 1            E7    4            F6    7            G5    0
Cl                 1            E8    4            F7    7            G6    0

E1             1.06999987
E2             1.06999978
E3             1.54000000
E4             1.07000000
E5             1.07000000
E6             1.07000000
E7             2.20000000
E8             2.20000000
F1           120.00007951
F2           119.99972580
F3           109.47120255
F4           109.47120255
F5           109.47123134
F6            90.00004829
F7            90.00004855
G1           180.00000000
G2            59.99830388
G3           179.99831867
G4           -60.00168873
G5            29.99845985
G6          -150.00183223
<- blank line
<- blank line
<- blank line
<- blank line


Perfectly, Gaussian ends with: EXPERIENCE IS THE FRUIT OF THE TREE OF ERRORS.

Instead of rangsiman’s hint to add the freq keyword to your input line, I would suggest you to do it additionally and not as the combination opt freq as the latter can lead to problems by not copying your whole input into the frequency calculation.

• Is there a reason you used 4 blank lines? Afaik two of them are interpreted by Gaussian as end of input file. – DSVA Aug 8 '17 at 11:53
• I just go straight to the end of any input that I write and add a random number of blank lines >= 3. So less could also work, yes. – pH13 - Yet another Philipp Aug 8 '17 at 11:55