![]() I specified a checkpoint file to use in my input file, : Suppose I have just completed a geometry optimization of water. Round/do-not-round Z-matrix parameters to the nearest 0.01 Angstrom and 1 degree.Īpply/do-not-apply full molecular symmetry to the system. Generate connectivity information (for PDB files, etc) using standard radii to figure out what atoms are bonded When generating connectivity information (for PDB files, etc) all atoms will be bonded Input angles are specified in radians (the default is degrees)įor a molecule destined for -ozmat and geometry optimization, allows interactive specification of constraints.įor a molecule destined for -ozmat, allows interactive specification of route, title, and charge/multiplicity lines. Input distances/coordinates are specified in Bohr (the default is Angstrom) The value you supply for N specifies which step in a geometry optimization for which you wish to extract a molecule specification. You can only use this option when your input file is a Gaussian checkpoint file. ![]() For a complete list, please see the Gaussian 98 User Guide. The following table lists some - not all - of the often used additional options which newzmat will accept. In other words, the following command will produce the same results as the prior:Īdditional options which do not involve the file format are summarized in the next section. If you do not provide filename extensions for the file names, newzmat will append the default extension listed in the table. Notice that the Program Option from the table is appended to the input or output option prefix: -i format and -o format, respectively. You should use the Program Option that appears in the chart above for these purposes a sample command which reads from a Protein Data Bank file and outputs a Gaussian Z-matrix file follows: The options that you will use most often are those which specify what format to use for the input file and what format to use for the output file. com file and writing to that same format. If you specify no options, the program defaults to reading from a Gaussian. to Brookhaven)Īfter you've run the setg98 input_file_name output_file_name MacroModel data file (formatted or unformatted) Gaussian input file (Cartesian specification) Gaussian input file (Z-matrix specification) The newzmat program supports reading and writing from and to the following file formats: This utility can convert molecule specifications between many different file formats, and can also extract the geometry at any optimization step from a checkpoint file. This document gives a short tutorial on the usage of the Gaussian utility program, newzmat.
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