The file names for DISCOVER files can be
file_name.arc. The base name is used to
construct the file name
file_name.hessian (the file with frequencies
and normal coordinates). All necessary data are extracted from these files.
The necessary data are collected from the
GAMESS output files are first checked for the occurrence of the string
GAMESS. If it is found the necessary data are collected from this file.
- GAUSSIAN 9X
Gaussian output files are first checked for the occurrence of the string
Entering Gaussian System. If it is found the necessary
data are collected from this file. To use the wave function related topics in
VIEWMOL with GAUSSIAN outputs GAUSSIAN must run with
Iop(5/33=1)3 to print basis set and MO coefficients. Due to the vastly different
outputs created by the GAUSSIAN 9X series of programs, it is not guaranteed
that a particular output can be successfully read. The common types of output have
been tested, but non-default routes through the program might have generated
output which cannot be read.
VIEWMOL first checks for the presence of a file with the extension
and the same basename as the MOPAC output file. This file is generated if
MOPAC has been run with the keyword
GRAPH. If such a file is found
coordinates, basis functions, and MO coefficients are read from this file. If such
a file does not exist, coordinates are read from the MOPAC output file under
CARTESIAN COORDINATES. Finally, vibrational frequencies and normal
modes are read from the MOPAC output file, if present.
- PDB files
Only the cartesian coordinates and atomic symbols are read from this file,
the connectivity information is ignored and will be determined by VIEWMOL
Coordinates are read from the section identified by
Forces, the energy, vibrational frequencies, and normal modes are collected from
the corresponding sections of the output.
The program reads the following data groups from the
The basis functions are read from these data groups. These data will be read
only if they are available.
These data group are read to determine which molecular orbitals are occupied
by how many electrons. The data is necessary for the calculation of electron
The cartesian coordinates of the molecule calculated. This data group
must be available.
The cartesian coordinates and gradients of all previous steps of a geometry
optimization. This data group will be read only if it is available.
The symmetry labels, energies, and MO coefficients for closed shells are read
from this data group. These data will be read if they are available and if the
file contains either converged or first order molecular orbitals.
The symmetry labels, energies, and MO coefficients for open shells are read
from this data group. These data will be read if they are available and if
the file contains either converged or first order molecular orbitals.
The point group of the molecule. This data group will be read only if it is
The title of the calculation. This data group will be read only if it is
$vibrational normal modes
The results of a force constant calculation. These two data groups will be read
only if they are available.
- GAUSSIAN 98 seems to have
a bug with respect to this option - no MO coefficients are printed anymore.
Use Iop(5/33=2) instead which, unfortunately, also prints the density
Jörg-Rüdiger Hill Fri Oct 31 14:19:21 CET 2003