Gaussian 03 Online Manual
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newzmatThe newzmat utility was designed primarily for converting molecule specifications between a variety of standard formats. It can also perform many related functions, such as extracting molecule specifications from Gaussian checkpoint files. Its full set of capabilities includes the following:
Command Syntaxnewzmat has the following general syntax: newzmat option(s) input-file output-file where option(s) is one or more options, specifying the desired operations, input-file is the file containing the structure to be converted (or retrieved), and output-file is the file in which to place the new molecule specification (or Gaussian input). Either filename may be replaced by a hyphen to denote standard input or standard output, as appropriate. If the output filename is omitted, it is given the same base name as the input file, along with a conventional extension denoting its file type. In general, extensions can be omitted from file specifications provided that extension conventions are followed. The default extensions are listed in the following table:
Input and Output OptionsThe options specifying the formats of the input and output molecule specifications are formed from the string -i or -o (respectively), followed immediately by the appropriate option form string from the preceding table corresponding to the desired molecule specification format (no spaces intervene). For example, -ipdb indicates that the input molecule specification is in PDB format and that the extension .pdb should be applied to the input filename if no extension is specified. Similarly, -oxyz specifies an output format of cartesian coordinates along with a default extension of .xyz for the output filename. The default input and output options are -izmat and -ozmat. Note that -izmat and -icart are synonyms, and either one of them can read a Gaussian input file containing any molecule specification format: Z-matrix, Cartesian coordinates, or mixed internal and Cartesian coordinates. Other Options Related to Input and OutputThe following options further specify the input for newzmat: -step N This option is not available for optimizations in redundant internal coordinates (the default coordinate system). Instead, retrieve the structure from the checkpoint file in a subsequent job by using a route section containing Geom=(Check,Step=N). -ubohr -urad The following options further specify the output file format: -mof1 -mof2 -optprompt -prompt ExamplesThe following command reads the molecule specification from the PDB file water.pdb and writes a Gaussian input file, including the equivalent Z-matrix, to the file h2o.com: $ newzmat -ipdb water h2o -ozmat is the default, so it can be omitted. Charge and multiplicity [0,1]? A return accepts the default values shown. newzmat prompts for the charge and multiplicity for the Z-matrix since these items cannot be determined from the PDB file. The following command reads the molecule specification from the Gaussian 03 checkpoint file G98-11234.chk and writes the PDB file propell.pdb: $ newzmat -ichk -opdb G98-11234 propell The following command reads the molecule specification from step 5 of the optimization from the checkpoint file newopt.chk and produces the Mopac file step5.inp: $ newzmat -ichk -omopac -step 5 newopt step5 The following command prints the molecule specification found in the checkpoint file mystery.chk and displays it in Gaussian input file format on the terminal screen (assuming the command is executed interactively): $ newzmat -ichk mystery.chk - The following command creates the checkpoint file quick.chk from the Gaussian input file that the user types in interactively: $ newzmat -ochk - quick # anything 0 1 O H 1 1.0 H 1 1.0 2 120. Blank line ends the input file. ^D Note that the input file must end with a blank line. The following command reads the molecule specification from the Mopac file newsalt.inp and writes a Gaussian input file including the equivalent Z-matrix to the file newsalt.com, prompting for the route and title sections and the charge and spin multiplicity for the molecule: $ newzmat -imopac -prompt newsalt Percent or Route card? # B3LYP/6-31G(d,p) Opt Route card? End route section with a blank line. Titles? Optimization of caffeine at B3LYP/6-31G** Titles? End title section with a blank line. Charge and Multiplicity? 0,1 Selecting an Output FormatIn order to communicate with a non-supported visualization system, the first choice of format to try is the PDB file. This format includes the connectivity information and is widely supported. Note that some software packages use the .ent extension, rather than .pdb; the -ient and -oent options select the former, while -ipdb and -opdb select the latter. Another commonly used alternative is the Mopac file format. Other newzmat OptionsThe other options to newzmat are concerned with generating connectivity information, with the use of standard geometrical parameters, and with the determination and use of molecular symmetry. A complete connectivity table can be used to generate Z-matrix specifications suitable for inclusion of symmetry constraints. Such a table is also required for output of the data files for the molecular mechanics programs. If one of the input formats which includes full connectivity is used (e.g., MacroModel data files), the connectivity that it provides is used. However, when Z-matrix or MOPAC format input is provided, only the connectivity information which is implied by the internal coordinate specification is available. Thus if a new Z-matrix which incorporates the molecular symmetry is to be generated, the remaining connectivity information must be generated. When cartesian coordinates are read in, naturally, no connectivity information is provided, so the default is to generate the table using the internally stored atomic radii. In addition, when used to generate input structures, the mechanics programs may not generate suitable bond distances and often produce coordinates which are close to but not exactly symmetric. Options control how each of these cases is handled. -allbonded -bmodel -density N -fudge -gencon -getfile -lsymm -mdensity
M -nofudge -nogetfile -noround -nosymav -nosymm -order -round -symav -symm -tsymm -rebuildzmat Known Difficulties with newzmat
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