Use macromodel format 2 (this is default if -ommodel is specified). Use macromodel format 1 (only valid with -ommodel). The following options further specify the output file format: Input angles in input stream are specified in radians (the default is degrees). Input distances in input file are specified in Bohr (the default is Angstroms). Instead, retrieve the structure from the checkpoint file in a subsequent job by using a route section containing Geom=( Check,Step= N). This option is not available for optimizations in redundant internal coordinates (the default coordinate system). Use the structure from step N of the geometry optimization data in a Gaussian 03 checkpoint file (valid only for the - ichk input option). The following options further specify the input for newzmat: Other Options Related to Input and Output 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. The default input and output options are -izmat and -ozmat. Similarly, -oxyz specifies an output format of cartesian coordinates along with a default extension of. pdb should be applied to the input filename if no extension is specified. For example, -ipdb indicates that the input molecule specification is in PDB format and that the extension. The 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 crystal structures (requires exactly 3 trans. MacroModel data file (may be formatted or unformatted)įractional coords. The default extensions are listed in the following table: Extension In general,Įxtensions can be omitted from file specifications provided that extension conventionsĪre followed. If the output filename is omitted, it is given the same base name as the inputįile, along with a conventional extension denoting its file type. Either filename may be replaced by a hyphen to denote standard input or standard output, as appropriate. 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). Newzmat option( s) input-file output-file Newzmat has the following general syntax: Newzmat can retrieve intermediate structures from a checkpoint file from (or during) a geometry optimization, for reuse or display. This capability can be used to extract data for display with a visualization package. Newzmat can also generate Gaussian 03 checkpoint files from other data files, and (more importantly) generate the data files from checkpoint files. The resulting data files have the proper symmetry constraints for efficient computation (if applicable). newzmat can thus be used to produce Gaussian input from the data files of many popular graphics and mechanics packages, allowing them to act as graphical input front-ends to Gaussian. This includes generating a Z-matrix (and hence input for Gaussian) from the files produced by other programs and also converting between the file formats of any of these programs. Newzmat can convert molecule specifications between a variety of data file formats. Its full set of capabilities includes the following: It can also perform many related functions, such as extracting molecule specifications from Gaussian checkpoint files. The newzmat utility was designed primarily for converting molecule specifications between a variety of standard formats.
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