Jaguar Input File Format

The input file should have the following format, where square brackets denote optional entries, and entries in italics represent a character string with no spaces:

[comments]
[MAEFILE:name.mae[gz]]
[BASISFILE:name.basis]
[ATOMIGFILE:name.atomig]
[DAFFILE:name.daf]
[GRIDFILE:name.grid]
[CUTOFFFILE:name.cutoff]
[PBFRADIIFILE:name.ark]
[GPTSFILE:name]
[PBFPRMFILE:name]
{sections describing molecule & calculation} 

The Maestro file specification (MAEFILE) is often included in the input file. It gives the location of the Maestro file that contains the structures corresponding to those in the Jaguar input file. The bonding information (“connection table”) from this file is used as the basis for any Lewis structures that are required for the calculation. Properties from this file are copied to the output Maestro file. It is recommended that you always use the Maestro file where possible, particularly for solvation calculations. If you do not use it, Jaguar constructs a Lewis structure from the coordinates, but this does not always produce optimal Lewis structures.

The last eight optional lines are only rarely used. Therefore, your Jaguar input files will generally take a form as simple as

{sections describing molecule & calculation} 

where only the zmat section, which contains the geometry, is actually required.

The .basis, .atomig, .daf, .grid, .cutoff, and .ark data files are described in Other Jaguar Files. If you want to use non-default choices for any of these files, you can specify their paths and names on the appropriate lines of the input file. If a file name ends with .Z (for example, BASISFILE: erwin.basis.Z), Jaguar copies the file and uncompresses it. You can specify a file on another host, or under another account name on that host, by listing the file name in the format host:fullpath or user@host:fullpath.

The GPTSFILE line allows you to use grid points and weights from an input file for any one grid used during the calculation. The file should have a line for each grid point, and each line should list, in order, the x, y, and z Cartesian coordinates (in angstroms) and the weight for that grid point. Grid weights are only used in charge fitting, so if you don’t want to use them, use 0 as a placeholder. For information about how to use this grid in a Jaguar calculation, see Grid and Dealiasing Function Keywords in the Jaguar Input File.

The PBFPRMFILE line allows you to specify the path to the parameter file for the Poisson-Boltzmann solver. The default file is $SCHRODINGER/jaguar-vversion/data/pbf.prm. This file contains parameters for the grids and numerical methods used.

Comments in the input file are ignored by Jaguar.