Using Gaussian 94/98 at NIST

This page is organized as follows:
I. Introduction
II. Syntax and a line by line description of a Gaussian input file.
III. Sample input files for H2O, HOCO, SF6 and C6H6.
IV. Build a Gaussian input file.
V. Visualizing the results with MOLDEN.

I. Introduction

This page is meant as an introduction and tutorial to using the Gaussian software - not as an all inclusive guide. You may follow this link to connect to GAUSSIAN, Inc. for the definitive guide on the net to using the software. It also contains a listing of ALL the keywords and their implementation.

If you are a :

  • NIST employee
  • guest worker
  • contractor
  • and you need additional assistance, e-mail Dr. Robert Bohn    (the author) or call at X-4731.

    II. Gaussian Input Files

    A Gaussian 94/98 input file has the following syntax:

  • Input lines have a maximum length of 80 characters.
  • Input is free-format and case insensitive.
  • Spaces, tabs, commas or forward slashes can be used in any combination to separate items within a line.  Multiple spaces are treated as a single delimiter.

  • Options to keywords may be specified in the following forms:

  •           keyword = option
              keyword=(option1, option2, ...)
              keyword(option1, option2, ...)
              Some keyword options can also take on values eg:   CBSExtrap(NMin=6)
  • All files end with a blank line !


    A basic GAUSSIAN input file has several different sections described below. Lines marked with a red asterisk (*) are required in every input file. Click on a link to get a more detailed explanation of a section.
    Link 0 Commands  Defines the location of scratch files and job resource limits. Begins with a % sign. Used in SF6 example.
    *Route Section Specifies the job type and model chemistry.  Begins with a # sign in the first column.
    *blank line Separates the route section from the title section.
    *Title Section Describes the job for the output and archive entry.
    *blank line Separates the title section from the molecule section.
    *Molecule Specification  Charge, spin and structure of the molecule to be studied.
    *blank line Separates the molecule section from the variable section OR End Of File.
    Variables Section Specifies values for the variables used in the molecule specification.
    blank line End of File if you use a variable section.

    ROUTE section

    The first line of the Route Section begins with a pound sign (#) in the first column. This line details the theoretical procedure you want to use, the basis set and the type of calculation. This is usually accomplished via two separate keywords within the route section of the input file, although a few method keywords imply a choice of basis set.

    Some procedures are:  HF (Hartree-Fock), RHF (Restricted Hartree-Fock), UHF (Unrestricted Hartree-Fock), and Density Functional Theory (DFT). The most commonly used standard basis sets are STO-3G, 3-21G, 3-21G*, 4-31G, 6-31G, 6-31G*, 6-31G**, 6-311G*, 6-311G** and 6-31G(d).

    This card also determines the way the output will be presented at the end of the run. There are 3 options for this.
    #T Terse option which is essential information and results.
    #P Additional output is generated. Includes messages at the beginning and end of each link giving machine dependent information as well as convergence information.
    #N or # Normal print level. This is the default.

    A few examples are of ROUTE cards are:
    # HF/STO-3G SP A single point (fixed geometry) Hartree-Fock energy calculation using an STO-3G basis set. The default if NO route card is given.
    #T RHF/6-31G A single point (fixed geometry) Restricted Hartree-Fock using the 6-31G basis set. RHF is used for closed shell restricted wavefunctions only. (multiplicity = 1) (terse output)
    # UHF/6-31G** A single point (fixed geometry) Unrestricted Hartree-Fock using the 6-31G** basis set. UHF is used for unrestricted open-shell wavefunctions. (multiplicity > 1) (normal output)
    #P RHF/6-31G(d) Opt Freq Geometry Optimization and vibrational frequency calculation using a Restricted Hartree-Fock with a 6-31G(d) basis set. (full output)
    #P B3LYP/6-31G(d) Opt Freq Geometry Optimization and vibrational frequency calculation using DFT with a 6-31G(d) basis set. The keyword for DFT is B3LYP for closed shell. For open-shell calculations use UB3LYP.


    TITLE section
    This section is required in the input, but is not interpreted in any way by the Gaussian program. It appears in the output for purposes of identification and description. Typically, this section might contain the compound name, its symmetry, the electronic state, and any other relevant information. The title section cannot exceed five lines and must be followed by a terminating blank line.

    The following characters should be avoided in the title section: @ # ! - _ \ and all control characters.

    MOLECULE specification

    This section contains specifics on the molecule namely its charge, multiplicity and initial geometry.

    The charge and multiplicity are on the same line and separated by a white space.

    Remember multiplicity = 2S+1 where S is the total spin. Alpha and Beta electrons have spins of +½ and -½, respectively. Equal numbers of each completely cancel and the total spin in that case is 0 and the multiplicity = 1 (singlet). An odd number of electrons gives at least spin = +½ and multiplicity = 2 (doublet).
    The entry for a neutral molecule in the singlet state is: 0  1
    The entry for a doublet anion (charge=-1) is: -1  2

    Defining a starting geometry for a molecule can be done in 2 ways; either in Cartesian coordinates or Z-matrix format. As you get more proficient in Gaussian, you will find that both formats have their pros and cons. Simple geometries tend to work well with Z matrices. With more complex geometries, you might find that Cartesian coordinates are more useful. You will just have try them out and then make up your own mind.

    In Cartesian format, the atom is defined in the following way:

    Element-label, x, y, z

    In Z-matrix format, the atom is defined in the following way:

    Element-label, atom 1, bond-length ,atom 2, bond-angle, atom 3, dihedral-angle

    The label is usually the elemental abbreviation with a secondary identifying integer: eg C1, C2 etc..

    Please note the following:

  • Default units for distances are in Å
  • Default units for angles are degrees
  • You may not define an angle or a distance as an integer - they are real numbers. Use "180.0" not "180".
  • The complete molecular specification for H2 (neutral,singlet) in Cartesian coordinates is :
    0   1
    H1  0.0    0.0   0.0
    H2  0.0   0.0   0.74

    The complete molecular specification for H2 (neutral,singlet) using the Z-matrix format is :
    0   1
    H2  1  0.74

    The value "1" in the last line denotes that the second atom, H2, is bonded (connected) to the first atom in the list.

    Input files for larger molecules (using Cartesian and Z-matrices) will be discussed in the section on Sample Gaussian Input Files.

    VARIABLE section

    One can use variable names for bond lengths, bond angles and dihedral angles as well. Going back to our example for H2 and use r=0.74 Å, we get a molecular specification that looks like:
    0   1
    H2  1  r1

    r1  0.74

    III. Sample Gaussian Input Files

    This section will describe sample input files (using Cartesian and Z-matrix formats) for H2O, HOCO, SF6 and C6H6.

    H2O   :   A Ground State Hartree-Fock Single Point calculation at 6-31G level.

    We know that this is a neutral molecule (charge=0) and has 1+1+8=10 electrons (5 alpha and 5 beta). Since the number of alpha and beta spin electrons are equal, this means the total spin = 0 and the multiplicity = 1.

    The complete structure of H2O can be determined by 2 equivalent OH bonds and the H-O-H bond angle. The experimentally determined structure yields r(OH) = 0.957 Å and a bond angle (BA) of 104.5°. But for sake of this discussion, let's make a "bad" guess and say that r(OH) = 1.0Å and BA = 90°. But this could also be a potentially useful calculation if one is investigating the potential energy surface of water. This will give the energy at this Single Point on the surface.

    Assuming the oxygen atom is located at the origin, the complete input files for both Cartesian and Z-matrix formats are:

    Route Section -> #HF/6-31G #HF/6-31G
    blank line    
    Title Section -> Water with Cartesian Water with Z-matrix
    blank line    
    charge, multiplicity -> 0 1 0 1
    Begin Molecule specification -> O1 0.0 0.0 0.0 O1
      H2 0.0 0.0 1.0 H2 1 rOH
    H3 is connected to atom 1 and makes an angle BA with atom 2. H3 1.0 0.0 0.0 H3 1 rOH 2 BA
    blank line (end for Cart)    
    Begin Variable definitions ->   rOH 1.0
        BA 90.0
    blank line (end for Z-matrix)    

    I did this calculation using Gaussian98 on The final SCF energy = -75.9697005 hartrees.

    What can one do next? You can calculate the ground state energy and optimized geometry of H2O and then make a comparison. But to get the optimized geometry, you'll have to read how to do it in the following section.

    HOCO   :   A Ground State Unrestricted Hartree-Fock Geometry Optimization calculation at 6-31G level.

    The answer to these questions can be ascertained through this calculation by seeing which one gives the lowest energy.

    This molecule is neutral (charge=0). It contains 1+8+6+8 = 23 electrons. Therefore it has 1 unpaired electron which contributes to the total spin. Using 2S+1 (S=½), multiplicity = 2. In other words, it is a doublet and we must do a UHF calculation. The entry for the charge and multiplicity for all 3 calculations is:

    0 2

    Without knowing what the structure is at first, we know that 4 atoms nominally exist in either a) cis, b) trans or c) linear arrangements. But we can create a table of initial guesses at the structures. You can get the dihedral angle from making a Newman Projection of the molecule.

    The questions we want to ask here are:

  • Which structure is the most stable ?
  • What is the optimized geometry of each configuration?
  • The answer to these questions can be ascertained through this calculation by seeing which one gives the lowest energy.

    Click Here to see the structures of all the different conformers.

      Cis HOCO Trans HOCO Linear HOCO
    R(O1H3) 1.0 Å 1.0 Å 1.0 Å
    R(O1C2) 1.35 Å 1.35 Å 1.35 Å
    R(C2O4) 1.2 Å 1.2 Å 1.2 Å
    a(H3O1C2) 135° 135° 180°
    a(O1C2O4) 135° 135° 180°
    dihedral(H3O1C2O4) 180°

    Case A: Cis-HOCO

    One can still set this molecule up in Cartesian coordinates. It's planar, so we only have to do 2-dimensional geometry to determine the proper coordinates. Click Here to see the actual set of computations you have to get the Cartesian coordinates. However, this is a case in which the Z-matrix format embarrassingly easy.

    The Molecule specification section (in bold) becomes a template for all conformers of this molecule. Only the title and variable sections are altered to generate the Z-matrices for the trans and linear cases.

    #UHF 6-31G OPT


    0 2
    C2 1 R12
    H3 1 R13 2 A312
    O4 2 R24 1 A124 3 DA

    R12   1.35
    R13   1.0
    R24   1.2
    A312   135.0
    A124   135.0
    DA   0.0

    Case B: Trans-HOCO

    #UHF 6-31G OPT


    0 2
    C2 1 R12
    H3 1 R13 2 A312
    O4 2 R24 1 A124 3 DA

    R12   1.35
    R13   1.0
    R24   1.2
    A312   135.0
    A124   135.0
    DA   180.0

    Case C: Linear-HOCO

    #UHF 6-31G OPT


    0 2
    C2 1 R12
    H3 1 R13 2 A312
    O4 2 R24 1 A124 3 DA

    R12   1.35
    R13   1.0
    R24   1.2
    A312   180.0
    A124   180.0
    DA   0.0

    The final values for the variables and the final energy for each conformer is tabulated below:

      Cis HOCO Trans HOCO Linear HOCO
    R(O1C2) 1.33024227 Å 1.34262179 Å 1.59856636 Å
    R(O1H3) 0.9594721 Å 0.95159027 Å 0.98162564 Å
    R(C2O4) 1.18933877 Å 1.1808501 Å 1.13782256 Å
    a(H3O1C2) 117.18485661° 115.49871545° 180.0°
    a(O1C2O4) 131.10877893° 128.65088481° 180.0°
    dihedral(H3O1C2O4) 180°
    Final Energy (hartree) -188.027641 -188.0291609 -187.9079994

    From this data, we can see that the Trans conformer of HOCO is the most stable. It lies (-188.0291609 + 188.027641 ) = -0.0015199 hartree lower than the cis form. Converting this to kcal/mole (1 hartree = 1.0987E4 kcal/mol) yields a difference of ~17 kcal/mole.

    SF6   :   A Ground State Hartree-Fock Geometry Optimization and Vibrational Frequency calculation at 6-31G* level.

    Again this molecule is a neutral, singlet. You should verify this yourself and determine the number of alpha and beta electrons this molecule has.

    The molecule has Oh symmetry and need only be defined by a single S-F bond (rSF) of 1.6Å and all the single F-S-F bond angles (aFSF) equal 90°.

    Click Here to get a view of the structure of SF6, the numbering system and how each line of the following Z-matrix is determined. Click on the Atom X link to get a description of how each line was generated.

    This is an excellent example of using a Link 0 command. We will use as the first line of the file a command which save the checkpoint file for future calculations.

    This file will keep copies of data that pertain to the calculation, like force constants. They will be useful starting points for future calculations. Remember that the force constants are related to the vibrational wavefunction and not the electronic wavefunction. Therefore using the results of a force constant calculation at a STO-3G level is a good place for starting a force constant calculation at a higher level of theory.

    %chk=sf6.chk Link 0 command to save the checkpoint file as "sf6.chk"
    SF6 HF/6-31G* geom opt with IR frequencies
    0 1 Charge Multiplicity
    S Atom 1
    F 1 r Atom 2
    F 1 r 2 90.0 Atom 3
    F 1 r 2 90.0 3 90.0 Atom 4
    F 1 r 2 90.0 3 180.0 Atom 5
    F 1 r 2 90.0 3 -90.0 Atom 6
    F 1 r 3 90.0 2 180.0 Atom 7
    r 1.6 Variables

    Alternatively, we can use the Cartesian coordinates for SF6. This is a case in which Cartesian coordinates are particularly easy. viz ...

    %chk = sf6.chk

    SF6 HF/6-31G* geom opt with IR frequencies

    0 1
    S1 0.0 0.0 0.0
    F2 1.6 0.0 0.0
    F3 0.0 1.6 0.0
    F4 0.0 0.0 1.6
    F5 0.0 -1.6 0.0
    F6 0.0 0.0 -1.6
    F7 -1.6 0.0 0.0

    The results of this calculation are:

    HF Energy (hartrees) = -993.9902203
    R = 1.554035 Å

    The results of the IR portion of the calculation yield 2 IR active bands at 644.7179 (T1u) and 1100.1456 (T1u) cm-1, respectively with relative intensity ratios of 1:27.27. Experimentally, the strongest absorption appears at 939 cm-1.

    The essence of this calculation shows that we calculated about 160 cm-1 too high. One could expect a better result by adding in d- and f-type or polarization functions by starting at a higher level of theory. In any event, we can still use the checkpoint file "sf6.chk".

    To use it in the next calculation, one would change the option on the OPT keyword. Above we calculated the force constants and now we need to read them. The new cards for calculation #2 would be:

    %chk = sf6.chk
    #P HF/6-311G** OPT=READFC FREQ

    SF6 HF/6-31G* geom opt w IR freqs. Second try.

    followed by the rest of the Molecular Specs.

    C6H6 : A Ground State Hartree-Fock Geometry Optimization calculation using Density Functional Theory (DFT) with a 6-31G(d) basis.

    Again, we start by knowing the charge here is 0 (a neutral). Then start counting the number electrons. But a-priori, we can tell that there is an even number because there are an equal number of atoms present. Therefore, the ground state is a singlet with multiplicity = 1.

    Now, I introduce the concept of "ghost" or "dummy" atoms. They are not involved in the calculation in any way. They are only there to use as an anchor for constructing a Z-matrix. It is labeled "X".

    For benzene, a good place to put the dummy atom is at the inversion center. Click here to see the molecule and it's numbering scheme. Here is the complete input file for running this job.

    %chk=ben.chk Link 0 command to save the checkpoint file as "ben.chk"
    #P B3LYP/6-31(d) OPT=(CALCFC,z-matrix)
    C6H6 HF/6-31G(d)
    0 1 Charge Multiplicity
    X Atom 1
    C2 1 rCC Atom 2
    C3 1 rCC 2 60.0 Atom 3
    C4 1 rCC 3 60.0 2 180.0 Atom 4
    C5 1 rCC 4 60.0 3 180.0 Atom 5
    C6 1 rCC 5 60.0 4 180.0 Atom 6
    C7 1 rCC 6 60.0 5 180.0 Atom 7
    H8 2 rCH 3 60.0 1 180.0 Atom 8
    H9 3 rCH 4 60.0 1 180.0 Atom 9
    H10 4 rCH 5 60.0 1 180.0
    H11 5 rCH 6 60.0 1 180.0
    H12 6 rCH 7 60.0 1 180.0
    H13 7 rCH 2 60.0 1 180.0
    rCC 1.4 Variables
    rCH 1.08

    #P HF/6-31(d) OPT=z-matrix
    rCC 1.4752 Å
    rCH 1.1087 Å
    HF=-229.8000165 hartrees

    IV. Build a Gaussian Input File

    This section will ask you to create some new Gaussian input files on your own. Answers will be provided by clicking on the links in this section.

    Problem 1. Create the input for NH3 at the STO-3G level of theory. You may use either Z matrix or Cartesian format.

  • N atom is at the origin (0,0,0).
  • r(NH)=1.0 Å
  • HNH angles = 120°
  • The H atoms lie 20° below the (x,y) plane.
  • Hint or Answer

    Problem 2. Create the input for a geometry optimization of (CH3)2CO (acetone) at the 6-31G level of theory. You may use either Z matrix or Cartesian format.

  • C atom is at the origin (0,0,0).
  • r(CC)=1.30 Å, r(CH)=1.08Å, r(CO)=1.20Å.
  • CCCO framework is planar. CCO angles=120°. CCC angle = 120°.
  • The CH3 group has a typical sp3 hybridized Carbon atom.
  • Hint or Answer

    Problem 3. Create the input for a vibrational frequency and geometry optimization of Li-cyclopentadienyl system, Li(C5H5). The Lithium atom lies directly over the center of the cylcopentadiene moiety. Use the 6-31G(d) level of theory.


  • C5H5 is planar.
  • CH bonds = 1.08Å
  • CC bonds = 1.4Å.
  • Angle (HCC) = 126°
  • Internal CCC angle = 108°
  • Li lies 1.40Å over the center of the C5H5 ring.
  • Hint or Answer

    V. Visualizing the results with MOLDEN

    MOLDEN is a visualization package that is installed on the machines in the Visualization Laboratory (Bldg 225, B131) and the Central Computing Facility machines (danube, arno, amur). This software is shareware which was downloaded from the Molden web site. You will find instructions there on how to use it and its features.

    Some of its visualization capabilities are:

  • Animate vibrational modes
  • Visualize reaction pathways
  • Visualize electron density plots and molecular orbitals
  • Simply, in order to use it with Gaussian, you must include this line in the ROUTE card:

    #P GFINPUT IOP(6/7=3)

    You may still add your other Keywords as necessary.

    Top of page