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, extensions can be omitted from file specifications provided that extension conventions are followed. 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. A slightly variant syntax is used when merging information from two files ( see below). 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 09 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.
Zmatrix input file gaussian full#
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.
0 kommentar(er)
