38.8 GOPENMOL -- calculate grids for visualization in gOpenMol
The syntax and sub-options are exactly the same as for CUBE, except
that the files produced are in a format that can be used directly in
visualization program. The following should be noted.
- Only the base name (up to the last '.') in filename is used,
and is appended by different suffices to create several different
- A CHARMm CRD-format file containing the coordinates is
always produced, and may be used in the invocation of gOpenMol:
- If DENSITY is given, then the file
is produced and contains the density grid in gOpenMol internal
- If ORBITAL is given, then for each orbital
specified, the file
is produced and contains the orbital grid in gOpenMol internal
- The default is not to produce any orbitals or densities, and so
only the atomic coordinates are dumped.
- The default is to use unformatted binary files, and this should
not normally be changed.
- The ORIGIN and AXIS commands should not be used.
is given in the input,
when all the grids have been calculated, an attempt is made to
start gOpenMol by executing the Unix command
rungOpenMol is not in $PATH, then nothing
Otherwise, gOpenMol should start and display the molecule. Any
.plt files produced can be added to the display by
following the Plot;Contour menu item.
The name of the Unix command may be changed from the default
rungOpenMol by specifying it as the first argument to the
By default, gOpenMol is not started, and this is equivalent to
giving the command BATCH.