The MSC Molecule Format
The MSC Molecule Format (MMF) is a flexible format for molecular
modeling. It is currently in revision 0.1. We plan to keep the format
backwards compatible provided that version numbers are included in the
Line One: Version Number
If line one contains the string:
then it is assumed that the file version is 0.1. If this line is
absent, it is assumed that the version is the most up-to-date
version. Currently, this is 0.1, so the line isn't particularly
meaningful. However, it will be used in future versions to insure
With the exception of the first line, any line that begins with a '#'
will be ignored.
Moreover, any totally blank line will be ignored.
Keywords for the MSC Molecule Format
- atom atno x y z
- Add an atom to the molecule. The user must specify the atomic
number atno, and the cartesian coordinates x,
y, and z. The coordinates are specified in
- orb lab en occ nterms
- Add an orbital to the molecule. The user must specify a label
lab (which can be arbitrary), an energy en,
and an occupation occ. If a nonzero number of
terms nterms is specified the subsequent nterms lines
will contain the basis function number ibf and the
coefficient coeff. If no terms are specified, the data
is saved for display purposes.
- bfn iat l nterms
- Add a (contracted) basis function to the molecule, specifying
the atom number atom of the origin (this many atoms must
already be specified) and the angular quantum number l
of the function (s=0, p=1, d=2, etc.). If a nonzero number of
terms nterms is specified, the following nterms lines
will contain the contraction coefficient icontr and the
exponent exp for this function.
- bond iat jat itype
- Add a bond to the molecule. If no bonds are specified, the bond
information will be generated from distances. The user must
specify the atoms iat and jat that comprise the
bond, and, optionally, the bond type itype.
- uc a b c alpha beta gamma.
- Specify unit cell information as a, b, c, alpha, beta,
- charge chg
- Set the charge of the molecule to chg.
- spin sp
- Set the spin of the molecule to sp.
- frag i j k l m n
- Specify atoms i,j,k,... as belonging to a fragment.
- fragbuff size
- Specify the buffer zone as extending over size Angstoms.