1E: Creating MOPAC input files

- By hand

As we have seen in the previous text, input files with z-matrices can be made entirely from scratch, in a text editor. For very simple molecules this is a feasible option.
The first three lines of the input file are reserved for one keyword line (however, see the 'keywords' + and &) and two comment lines. Very common keywords are AM1 (or PM3) as the method, a T=3600 time statement, NOINTER to limit the output.
Usually, the z-matrix starts on the fourth line, and is closed by a zero or empty line.

- Using a modelling program

For larger structures the use of a modelling program is required. A program like SYBYL offers a drawing module to sketch the structure, a force field to 'clean' it, and an interface to MOPAC which prepares an input file (Compute - Interfaces - MOPAC).
This interface produces a file with cartesian coordinates, not with a z-matrix. However, one simple run in MOPAC will suffice to obtain an .arc file, which includes a z-matrix at the end.
In command mode, through the command QCPE m1 MOPAC SETUP filename Z_MATRIX (molecule area and filename to be specified by user), SYBYL can be requested to produce a z-matrix, which can be edited, etc.
In the SYBYL MOPAC interface several options can be selected, which will be effected by adding keywords to the input file or changing the optimization flags.
It gives the choice between the 'internal' version of MOPAC, 5.0, or ('use other MOPAC') MOPAC93 as an external one. Through Netbatch the MOPAC calculations can be started directly, or the job can be held for later. This gives one the opportunity to make changes in or additions to the input file which can not be handled by the interface.

Exercise, to draw a structure, obtain a z-matrix and edit it to include the proper reaction coordinates for a Diels-Alder reaction.

The SYBYL/MOPAC combination produces a series of files, from which the results can be read and displayed by SYBYL (Analyze -Interfaces - MOPAC). This includes orbitals (if requested, see paragraph 3C), and vibrations, calculated with the keyword FORCE (see paragraph 2A).

- Using Babel

The conversion program BABEL is able to prepare MOPAC input files, using internal coordinates, from a large series of other types of files, among which the SYBYL mol2 format. This the format in which SYBYL stores a structure.

The .mol2 file of butene looks like this:

#	Name:			
#	Creating user name:	borkent
#	Creation time:		Thu Nov  3 11:54:03 1994

#	Modifying user name:	borkent
#	Modification time:	Thu Nov  3 11:54:34 1994

@MOLECULE
****
   12    11     1     1     1
SMALL
USER_CHARGES


@ATOM
      1 C1_____    -5.4733    1.0358    0.0000 C.3       1 <1>        0.0000 
      2 C2_____    -4.3613    2.1157    0.0000 C.3       1 <1>        0.0000 
      3 C3_____    -2.9799    1.5063    0.0000 C.2       1 <1>        0.0000 
      4 C4_____    -1.8777    2.2655    0.0000 C.2       1 <1>        0.0000 
      5 ****       -6.4663    1.5125    0.0000 H         1 <1>        0.0000 
      6 ****       -5.3879    0.4007    0.8957 H         1 <1>        0.0000 
      7 ****       -5.3879    0.4007   -0.8957 H         1 <1>        0.0000 
      8 ****       -4.4721    2.7506    0.8942 H         1 <1>        0.0000 
      9 ****       -4.4721    2.7506   -0.8942 H         1 <1>        0.0000 
     10 ****       -2.8691    0.4206    0.0000 H         1 <1>        0.0000 
     11 ****       -0.8861    1.8124    0.0000 H         1 <1>        0.0000 
     12 ****       -1.9487    3.3530    0.0000 H         1 <1>        0.0000 
@BOND
     1    2    1 1    
     2    2    3 1    
     3    3    4 2    
     4    1    5 1    
     5    1    6 1    
     6    1    7 1    
     7    2    8 1    
     8    2    9 1    
     9    3   10 1    
    10    4   11 1    
    11    4   12 1    
@SUBSTRUCTURE
     1 ****        2 TEMP              0 ****  ****    0 ROOT 
@SET
ATOM$CYAN       STATIC     ATOMS    COLORGROUP SYSTEM 
4 1 2 3 4
@NORMAL
@FF_PBC
FORCE_FIELD_SETUP_FEATURE Force Field Setup information
v1.0  0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 NONE 0 0 0 0 0 0 0 0 0 0 0 0 0

and the converted .dat file:

KEYWORDS GO HERE
test.dat
test.dat
 C    0.0000000  0      0.000000  0      0.000000  0    0    0    0      0.0000
 C    1.5500735  1      0.000000  0      0.000000  0    1    0    0      0.0000
 C    1.5098458  1    112.034513  1      0.000000  0    2    1    0      0.0000
 C    1.3383682  1    121.636252  1    180.000000  1    3    2    1      0.0000
 H    1.1014953  1    110.195207  1    180.000000  1    1    2    3      0.0000
 H    1.1013281  1    110.250342  1     60.097248  1    1    2    3      0.0000
 H    1.1013281  1    110.250342  1    -60.097248  1    1    2    3      0.0000
 H    1.1022560  1    109.218630  1   -120.781537  1    2    1    3      0.0000
 H    1.1022560  1    109.218630  1    120.781537  1    2    1    3      0.0000
 H    1.0913391  1    119.631602  1      0.000000  1    3    2    1      0.0000
 H    1.0902157  1    120.883290  1    180.000000  1    4    3    2      0.0000
 H    1.0898152  1    120.823846  1      0.000000  1    4    3    2      0.0000