The zmat, zmat2, and zmat3 Sections of the Jaguar Input File
- Overview
- Examples
The molecular geometry must be described in the zmat section. Details on entering a geometry through the GUI can be found in Editing Jaguar Input Files and Setting Up a Jaguar Input File. The units for the geometry are set by the iunit keyword of the gen section; by default, these units are angstroms and degrees.
If the geometry is in Cartesian coordinates, each line must contain four items: an atom name and the (x, y, z) coordinates. Each item should have at most 80 characters. The atom name should begin with the one- or two-letter element symbol, in either uppercase or lowercase characters. Other alphanumeric characters may be added, as long as the atomic symbol remains clear—for instance, HE5 would be interpreted as helium atom 5, not hydrogen atom E5. Up to eight characters can be given in an atom name.
A sample Cartesian zmat section for a water molecule is:
&zmat O 0.000000 0.000000 -0.113502 H1 0.000000 0.753108 0.454006 H2 0.000000 -0.753108 0.454006 &
The geometry can also be specified in internal coordinates—see Z‑Matrix Format for Jaguar Geometry Input. It can also be in a mix of Cartesian and internal coordinates.
If your input comes from the PDB, you may need to change some of the atom labels. An atom label like “CA” denotes calcium in the zmat section, but this symbol is the conventional PDB label for an alpha carbon in an amino acid residue. If you want to use PDB atom names in a Jaguar input file, you must insert an underscore after the atomic symbol, so that for example the alpha carbon would be represented as “C_A”. When the Jaguar input file contains a reference to a Maestro structure file, which is always the case when the input file is created using Maestro, a check will be performed to ensure consistency between the atomic symbol used for the atom label, and the atomic number. Thus, an atom label of “CA” whose associated atomic number is 6 produces an error.
A zmat section in Z‑matrix format should not include lines defining variables (which are set in the zvar section described in The zvar, zvar2, and zvar3 Sections of the Jaguar Input File), and should not contain any comment lines, but otherwise should have the same format as described in Z‑Matrix Format for Jaguar Geometry Input, Variables and Dummy Atoms in Jaguar Z‑Matrix Input, and Constraining Z‑Matrix Bond Lengths or Angles in Jaguar Input. Constraining Z‑Matrix Bond Lengths or Angles in Jaguar Input also includes a description of how to specify bond length or angle constraints on the Z‑matrix coordinates for geometry optimizations.
You can orient the molecule or system using a label on the same line as the zmat section label. This orientation label should begin with the word orient, which is followed by an option in the form ab, −ab, a−b, or −a−b, where a and b are each either x, y, or z (for example, &zmat orient x‑y). Jaguar places the first atom in the Z‑matrix at the origin, the second along the a-axis (in the negative direction for −a), and the third atom in the ab plane, in the quadrant determined by the positive or negative signs of a and b.
To perform counterpoise calculations, you can specify counterpoise atoms, which have the usual basis functions for that element but include no nuclei or electrons, by placing an @ sign after the atom labels. For example, to place sodium basis functions at the Cartesian coordinates (0.0, 0.0, 1.0), you could include the following line in a Cartesian input file:
Na1@ 0.0 0.0 1.0
You can also input counterpoise atoms for geometries in Z‑matrix format.
If you are optimizing a molecular structure to obtain a minimum or a transition state, you might want to refine the Hessian used for the job. (See Transition-State Optimizations for information on the methods used for transition-state optimizations, including Hessian refinement.) If you add an asterisk (*) to a coordinate value, Jaguar computes the gradient of the energy both at the original geometry and at a geometry for which the asterisk-marked coordinate has been changed slightly, and will use the results to refine the initial Hessian to be used for the optimization. (To request refinement of a coordinate whose value is set using a variable, add an asterisk (*) to the end of the variable setting in the zvar section line that defines the variables.) For instance, a job that included Hessian refinement that was run with the following zmat section would use both O–H bonds and the H–O–H angle in the refinement:
&zmat O1 H2 O1 1.1* H3 O1 1.1* H2 108.0* &
Molecular symmetry or the use of variables, either of which may constrain several coordinate values to be equal to each other, can reduce the number of coordinates actually used for refinement. For instance, for the water input example shown above, only two coordinates will actually be refined (the O–H bond distance, which is the same for both bonds, and the H–O–H angle) if molecular symmetry is used for the job.
Some types of transition-state optimizations require two or three geometries (see Transition-State Optimizations). For these jobs, you can input the second and third geometries (Geometry 2 and Geometry 3) in the zmat2 and zmat3 sections. The order of atoms in the input must be the same as in the zmat section. Alternatively, if the changing coordinates in the zmat section are set using variables, you can leave out the zmat2 and zmat3 sections and specify the second and third geometries by adding zvar2 and zvar3 sections, which will be used in combination with the zmat section to define the second and third geometries. See The zvar, zvar2, and zvar3 Sections of the Jaguar Input File for details.
Single Point Energy Examples
Transition State Geometry Optimization Examples
Example: B3LYP-D3/6-31G** TS optimization for amide hydrolysis. Apply the quadratic synchronous transit (QST) search algorithm that uses the reactant, product, and transition state structure as a guess
&gen igeopt=2 iqst=1 itrvec=-5 dftname=B3LYP-D3 basis=6-31G** & &zmat C1 0.0495980000000 0.2533700000000 -0.3607110000000 C2 1.4197410000000 0.2878870000000 0.2842060000000 O3 2.2207240000000 1.2032400000000 0.2164680000000 N4 2.1467540000000 -1.3358890000000 0.0333660000000 C5 3.5632580000000 -1.2838090000000 -0.3163310000000 H6 4.1158520000000 -2.1250250000000 0.1140940000000 H7 -0.4763550000000 -0.6831700000000 -0.1651180000000 H8 -0.5415720000000 1.0753480000000 0.0506750000000 H9 0.1518600000000 0.4065490000000 -1.4388620000000 H10 1.6081090000000 -1.9865110000000 -0.5310510000000 H11 3.6993010000000 -1.2866820000000 -1.4018320000000 H12 3.9603300000000 -0.3414190000000 0.0702700000000 O13 1.1762500000000 -0.3300010000000 1.7855610000000 H14 1.8708550000000 -1.2482310000000 1.1298150000000 H15 1.6182900000000 0.3172350000000 2.3567090000000 & entry_name2: reactant &zmat2 C1 0.2183000000000 0.2197920000000 -0.5170720000000 C2 1.6171140000000 0.1603480000000 0.0649390000000 O3 2.2489110000000 1.1546850000000 0.3754610000000 N4 2.2587850000000 -1.1023090000000 0.0211870000000 C5 3.5667470000000 -1.1818210000000 -0.6303440000000 H6 4.0512400000000 -2.1268260000000 -0.3715750000000 H7 -0.4157050000000 -0.5937250000000 -0.1597090000000 H8 -0.2405490000000 1.1723010000000 -0.2511220000000 H9 0.2987020000000 0.1576110000000 -1.6096780000000 H10 1.6244180000000 -1.8506820000000 -0.2376340000000 H11 3.5025230000000 -1.1047410000000 -1.7246620000000 H12 4.1807810000000 -0.3612210000000 -0.2579850000000 O13 0.7738580000000 -0.4704350000000 2.1755670000000 H14 1.6301480000000 -0.9058390000000 1.8977370000000 H15 1.0664630000000 0.3258540000000 2.6385140000000 & entry_name3: product &zmat3 C1 0.0728300000000 0.3145440000000 -0.4134690000000 C2 1.2539580000000 0.4686730000000 0.5052290000000 O3 2.1169230000000 1.3158960000000 0.4126330000000 N4 2.3144340000000 -1.5775530000000 0.0007060000000 C5 3.6689680000000 -1.4275930000000 -0.5002000000000 H6 4.3859260000000 -2.1895890000000 -0.1509490000000 H7 -0.4034160000000 -0.6586410000000 -0.2985600000000 H8 -0.6564980000000 1.0912100000000 -0.1489020000000 H9 0.3857450000000 0.4691010000000 -1.4452860000000 H10 1.8719330000000 -2.4265180000000 -0.3320280000000 H11 3.6591630000000 -1.4676670000000 -1.5951720000000 H12 4.0472370000000 -0.4425370000000 -0.2089700000000 O13 1.1199000000000 -0.2596670000000 1.6884280000000 H14 2.1162020000000 -1.3719070000000 0.9864270000000 H15 1.5415760000000 0.2825940000000 2.3744100000000 & &connect C2 O13 N4 H14 C2 N4 O13 H14 &
$SCHRODINGER/jaguar run -jobname=opt_ts_qst_0001 opt_ts-qst-0001.in