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27.13 GAUSSIAN Command — Invoke Gaussian Program

The GAUSSIAN command is used to invoke the Gaussian program1 Currently, this interface may only be used to calculate partial charges for fragments of the system. It uses the Gaussian 94 program to calculate the wavefunction and electrostatic field for the fragment. Four different methods are provided for calculating partial charges from the wavefunction. All of these methods determine partial charges by performing a least squares fit of the potential generated by the partial charges to the potential calculated using the wavefunction. The fundamental difference between the methods is the layout of points where the electrostatic potential is determined by the wavefunction, and subsequently used for the least squares fit of atomic charges.

The first method, PDM, uses two programs written by Don Williams, PDM88 and PDGRID.23 The PDGRID program lays out a grid of points around the fragment where the potential will be calculated, and the PDM88 program does the least squares fit to determine the best values for the partial charges.4 The other methods have been incorporated directly into Gaussian 94, and use different grid layouts. There is the scheme due to Merz, Singh, and Kollman,56 identified by the keyword, MK; the scheme due to Chirlian and Francl,7 identified by the keyword, CHELP; and the scheme to Breneman and Wiberg,8 identified by the keyword, CHELPG.

All of these schemes have their own values for van der Waals radii encoded within them. However, the default in this interface is to use the radii from the parameters in CONGEN. If you want to use the radii in the external programs, use the EXTRADII keyword.

This command simplifies the use of these three programs. You specify the atoms you want charges for, and the programs are invoked in turn to calculate the charges. Remember that the time for the calculation increases approximately with the fourth power of the number of electrons. A number of files are generated when this command is executed. Normally, these files are deleted after the command is complete, but you can request that they be saved.

Note that the collection of atoms that you specify should be a complete molecule including hydrogens. It does not make physical sense to do anything different, although the program does not check for completeness.

If you use this command to calculate results that are eventually published, please ensure that both Gaussian 94 and the fitting scheme you use is properly referenced.

27.13.1 Syntax

     GAUSsian CHARges {SELECT atom-selection END}
              [BASIs word] [SCF word] [TOTAl real] [MEMOry int]
              [UNIT unit] [PREFix word] [EXTRadii] [DIPOle]
              [PDM [UNDEr real] [SHELl real] [SPACing real] ]
              [MK                                           ]
              [CHELP                                        ]
              [CHELPG                                       ]
              [STEPs repeat(step-options) END]
              [SAVE] [NORUn]
              [MERGe atom-selection END]
              repeat( AVERage atom-selection END )
                     [ ALL           ]
                     [ NONE          ]
                     [ [NO]CREAte    ]
                     [ [NO]HF        ]
     step-option ::= [ [NO]GRID      ]
                     [ [NO]POTEntial ]
                     [ [NO]FIT       ]
                     [ [NO]SCAN      ]
                     [ [NO]DELEte    ]

See Atom Selection, for the syntax of an atom-selection.

27.13.2 Function

The GAUSSIAN command functions by writing a set of input files for Gaussian, PDGRID, and PDM88; preparing a Bourne shell script to execute each program in turn; executing the script; and reading the results. The options are interpreted as follows:

This keyword must be specified. It is anticipated that other functions of GAUSSIAN will be invoked in the future.
The SELECT keyword is used to demark an atom-selection that identifies the atoms to be selected. By default, no atoms are selected, so you must specify something.
The word which follows BASIS gives the basis set to be used by Gaussian. The default is 6-31G.
The SCF option is used to replace the DIRECT and QC keywords to the SCF command in Gaussian.
The TOTAL option specifies the total charge of the fragment. The default is zero.
This specifies the number of words of memory to be allocated to Gaussian. This option is used for the %mem keyword. The default is 5000000.
This option is used to specify the Fortran unit for all I/O done by this command. The default is 99.
This option specifies the file name prefix to use for all the intermediate files generated by this command. The default is cgq_<pid> where <pid> is the current process id.
This option specifies that the atomic radii in the external programs be used. Normally, CONGEN supplies the programs with the van der Waals radii from the parameter file.
This keyword indicates that the PDM programs of Don Williams should be used.
This keyword specifies the distance under the van der Waals radii for grid points to be placed. The default is 0.0, which means that no points are placed under the van der Waals radius. This option is used only if the PDM option is selected.
This keyword specifies the spacing between grid points. The default is 0.8 Angstroms. This option is used only if the PDM option is selected.
This keyword specifies the maximum distance of any grid point to the van der Waals surface of a molecule. This option is used only if the PDM option is selected.
This keyword specifies that the Singh, Besler, Merz and Kollman gridding scheme should be used.
This keyword specifies that the CHELP gridding scheme should be used. Note that this keyword may not be abbreviated.
This keyword specifies that the CHELPG gridding scheme should be used. Note that this keyword may not be abbreviated.
For the MK, CHELP, and CHELPG schemes, this option specifies that the fit of charges shall also consider the quantum mechanical calculation of the dipole moment.
This option requests that charges on the selected atoms be merged with the atoms that they are bound to. Only atoms which have exactly one bond can be treated this way, and this option was created primarily for use with hydrogens.
The AVERAGE options are used to average charges. They are most appropriate when certain atoms are symmetric, but are exposed to different electrostatic environments. You can specify as many AVERAGE options as needed, but the sets of atoms may not overlap within the system being analyzed. After the averaging and merging steps are performed, the program adjusts all the charges to bring the total to the value you have specified.
The STEPS option allows detailed control over the execution of the programs. CONGEN maintains a list of boolean variables which specify whether certain steps will be executed, and the STEPS option controls the setting of these variables. Each option is interpreted sequentially to affect the variables. The presence of the string, NO, preceding some of the keywords means that the variable should be turned off. The options are interpreted as follows:
Turn on all steps.
Turn off all steps.
Create all the input files and shell scripts necessary to run the charge calculation. If a particular step is omitted from the operation, the affected command in the shell script is commented out, so you can manually enable it by editing the script. In order to use this command effectively, you must use the same file prefix every time.
Perform the initial Hartree-Fock single point calculation. In all methods except PDM, this option also controls the steps up to the FIT step.
Execute PDGRID which lays out the grid where the electrostatic potential will be evaluated. This applies only to the PDM option.
Calculate the electrostatic potential on the grid points from the wave function. This applies only to the PDM option.
Invoke PDM88 which fits the charges to the calculated potential. This applies only to the PDM option.
Scan the results from the calculations back into CONGEN.
Delete intermediate files.

This option requests that all intermediate files be saved after the command runs. It has the same effect as STEPS NODELETE END option. Normally, all intermediate files are deleted.
This option requests that all initial input files be saved and not executed. This is useful when you want to modify the Gaussian and PD input files created by the program. Note that this option complete overrides the settings in the STEPS option.

The following table gives the file types for all the intermediate files used:

Gaussian checkpoint file
Hartree-Fock input
Hartree-Fock output
PDGRID input file
PDGRID output file
PDGRID grid specification
Electrostatic potential calculation input
Electrostatic potential calculation output
PDM88 input.
PDM88 output.
Filtered charge calculation output.
Shell script to run everything.
Output from shell.


[1] Gaussian 94, Revision E.2, M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. Keith, G. A. Petersson, J. A. Montgomery, K. Raghavachari, M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen, M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. P. Stewart, M. Head-Gordon, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1995.

[2] D.E. Williams, Quantum Chemistry Program Exchange, Program 568; PDM88 (which includes PDGRID)

[3] D. E. Williams, “Representation of the Molecular Electrostatic Potential by Atomic Multipole and Bond Dipole Models”, J. Comput. Chem. 9, 745-763 (1988).

[4] The program, PDM88, is obsolete. Although it serves the need for a charge calculation in CONGEN, the newer version has more features for those users interested in exploring charge calculations. For further information please contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA, Tel: (502)588-5975, Fax: (502)588-8149, E-mail: dewill01@ulkyvx.bitnet.

[5] U. C. Singh and P. A. Kollman, J. Comput. Chem., 5, 129 (1984).

[6] B. H. Besler, K. M. Merz, and P. A Kollman, J. Comput. Chem., 11, 431 (1990).

[7] L. E. Chirlian and M. M. Francl, J. Comput. Chem., 8, 894 (1987).

[8] C. M. Breneman and K. B. Wiberg, J. Comput. Chem., 11, 361 (1990).