Using the Gaussian newzmat Program J.T. Frey, 05/27/2001

This document gives a short tutorial on the usage of the Gaussian utility program, newzmat. 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.

  (1) File Formats
  (2) Command Format
  (3) Additional Options
  (4) Useful Examples

Supported File Formats
The newzmat program supports reading and writing from and to the following file formats:

Extension	File Type	Program Option
.bgf	Biograf internal data file	bgf
.cac	CaChe molecule file	cache
.chk	Gaussian checkpoint file	chk
.com	Gaussian input file (Z-matrix specification)	zmat
.com	Gaussian input file (Cartesian specification)	cart
.con	QUIPU system data file	con
.dat	Model/XModel/MM2 data file	model
.dat	MacroModel data file (formatted or unformatted)	mmodel ummodel
.ent	Brookhaven data file (equiv. to PDB)	ent
.inp	MOPAC input file	mopac
.pdb	Protein Data Bank format (equiv. to Brookhaven)	pdb
.ppp	Unknown program, output option only	ppp
.xyz	Plain Cartesian coordinates	xyz
.zin	Ancient version of ZINDO	zindo

Command Format
After you've run the setg98{.a9} command, the newzmat program is within the scope of your path and can be run. If when trying to run the command you're told that the program does not exist, then you probably forgot to run the setg98{.a9} command.

The command's syntax is simple:

newzmat {option(s)} input_file_name output_file_name

If you specify no options, the program defaults to reading from a Gaussian .com file and writing to that same format. 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. 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:

newzmat -ipdb -ozmat water.pdb water.com

Notice that the Program Option from the table is appended to the input or output option prefix: -iformat and -oformat, respectively. If you do not provide filename extensions for the file names, newzmat will append the default extension listed in the table. In other words, the following command will produce the same results as the prior:

newzmat -ipdb -ozmat water water

Additional options which do not involve the file format are summarized in the next section.

Additional Options
The following table lists some -- not all -- of the often used additional options which newzmat will accept. For a complete list, please see the Gaussian 98 User Guide.

-step N	You can only use this option when your input file is a Gaussian checkpoint file. The value you supply for N specifies which step in a geometry optimization for which you wish to extract a molecule specification.
-ubohr	Input distances/coordinates are specified in Bohr (the default is Angstrom)
-urad	Input angles are specified in radians (the default is degrees)
-optprompt	For a molecule destined for -ozmat and geometry optimization, allows interactive specification of constraints.
-prompt	For a molecule destined for -ozmat, allows interactive specification of route, title, and charge/multiplicity lines.
-allbonded	When generating connectivity information (for PDB files, etc) all atoms will be bonded
-gencon	Generate connectivity information (for PDB files, etc) using standard radii to figure out what atoms are bonded
-round/-noround	Round/do-not-round Z-matrix parameters to the nearest 0.01 Angstrom and 1 degree.
-symm/-nosymm	Apply/do-not-apply full molecular symmetry to the system.

Useful Examples

Extracting an Optimized Geometry

Suppose I have just completed a geometry optimization of water. I specified a checkpoint file to use in my input file, water.com:

% chk=water.chk
# b3lyp/6-31g opt

Optimized water molecule

0 1
H
O 1 1.05
H 2 1.05 1 110.0

The geometry specified in my input file does not reflect the optimal geometry; that geometry is given in both the water.log and water.chk files for the calculation. I wish to extract the optimized geometry from the checkpoint file and save it in a z-matrix input file which I will call waterOpt.com. The one question that comes to mind is: what step number should be specified to get the optimized geometry using newzmat? Luckily, the program is smart enough to recognize that a step number greater than or equal to the actual last step number in a checkpoint file for an optimization mean the same thing.

TIP: Specifying a large step number -- perhaps 99 or even 999 -- will force newzmat to read the optimized (last) geometry from a checkpoint file.

Thus, if I issue the command:

newzmat -ichk -ozmat -step 999 water waterOpt

then barring any errors the file waterOpt.com will contain a z-matrix for the optimized water molecule.