Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame in a COORDS set.

zmatrix <COORDS set name> [name <output set name>]
        { zset <input zmatrix set> [parm <top>|parmindex <#>] |
          [molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }

<COORDS set name> COORDS set to calculate Z-matrix from or use as topology for applied Z-matrix.
[name <output set name>] Name of output COORDS set (if ‘zset’) or output Z-matrix set.
zset <input zmatrix set> Name of Z-matrix set to use to generate coordinates.
parm <top> Use specified topology name as topology for generated coordinates.
parmindex <#> Use topology index as topology fo generated coordinates.
[molnum <mol#>] Calculate Z-matrix from specified molecule (default first molecule).
[frame <frame#>] Calculate Z-matrix from specified molecule in specified frame (default first frame).
[out <zmatrix file>] File to write calculated Z-matrix to.

Data sets created:
<output set name> If ‘zset’, COORDS set containing final coordinates. Otherwise contains Z-matrix data.

Command for working with Z-matrices. If zset is specified, generate coordinates from the specified Z-matrix data set and topology. Otherwise, calculate a Z-matrix for a single molecule from the specified frame of given COORDS data set.

For example, to generate the Z-matrix for a mol2 file:

parm MP1.mol2 name mp1
loadcrd MP1.mol2 parm mp1
zmatrix MP1.mol2 parm mp1 out zmatrix.dat