Program keywords

When  reading  a file for the first time, MOLDRAW writes at the end  of  the input  deck (the file with .MOL extension) information about the center of gravity (BARICE),  the    connectivity  (CONNB), the number of bonds for each  atom  (BONDS), the hydrogen bond contacts (CONNHB)  and the number of fragments (FRAG) of the corresponding  molecular  system.  These quantities  are read in in  all  subsequent  runs.  Whenever  a manual modification of the geometry  specification  is   performed (deletion of an atom or change of the value of a coordinate) all the added connectivity information  must be deleted from the input file; the geometry modification are then correctly taken into account in the subsequent runs.

It is however unlikely that the  user will manually change any connectivity information, which can be altered  by  means  of the LINK and UNLINK commands within the MOLDRAW session. However, a  brief  description of the program generated keywords follows:

BARICE: it defines the molecular center of masses. The molecule is centered with respect to this point.

Example:

BARICE

1.2345678  2.4527878  3.678119044

CONNB: it defines the atomic bond connectivity. The first record is the total number of bonds in the structure. Each pair of numbers defines the two bonded atoms.

Example:

CONNB
 24
 1 5 1 6 2 12 2 3 3 13 3 14 3 4 4 16 4 15 4 17 5 18 5 7 6 19 6 8 7 9
 7 21 8 9 8 20 9 10 10 11 10 21 11 23 11 22 11 24

In this case 24 bonds are present. Atom 1 is bonded to atom 5, atom 1  to atom 6, atom 2 to 12, etc.

BONDS:  it reports the total number of atoms bond to each atom.

Example:

BONDS
 2 2 4 4 3 3 3 3 3 3 4 1 1 1 1 1 1 1 1 1 2 1 1 1

In this case atom 1 is bonded to two atoms, atom 2 to two atoms, atom 3 to 4, etc.

CONNHB:  it reports which bond is involved in an H-bond. The value 0 is for non H-bond, 1 for H-bond.

Example:

CONNHB
 24
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0

In this case the bond number 21 is an H-bond.

FRAG: it reports the number of disjointed molecular fragments in the structure.

Example:

FRAG
 2
 1 2 2 2 1 1 1 1 1 1 1 2 2 2 2 2 2 1 1 1 1 1 1 1

In this case there are 2 molecular fragments and the same label identifies the fragment to which the corresponding atom belongs (atoms 1,4,5,.. belong to fragment 1; atoms 2,3,4,... belong to fragment 2).

ONIOM: reports the atoms belonging to the high-level model zone (atomic flag set to 1) and to the low level one (atom flag set to 0) in the definition of a ONIOM2 calculation.

Example:

ONIOM
 1   0
 2   0
 3   0
 4   0
 5   0
 6   1
 7   1
 8   1
 9   1
 10   0
 11   0
 12   0
 13   0
 14   0
 15   0
 16   0
 17   0
 18   0
 19   0
 20   0
 21   0
 22   0
 23   0
 24   0

In this case atoms 6,7,8,9 belongs to the high-level model zone, whereas all the other are in the low level region.

VIBRATIONS:  indicates that vibration normal modes are present in the file. The toatl number of normal modes is reported in the next record. For each normal mode, identified by the NMODE n keyword,  the FREQUENCY (cm-1), SYMMETRY, IR-INTENSITY and RAMAN-INTENSITY are reported. For each mode the cartesian displacements are reported.

Example:

VIBRATIONS
 30
FREQUENCY  411.2624
SYMMETRY E2U
IR-INTENSITY  0
RAMAN-INTENSITY  0
NMODE  1
 6             0             0             0
 6             0             0             .21
 6             0             0            -.21
 6             0             0             0
 6             0             0             .21
 6             0             0            -.21
 1             0             0             0
 1             0             0             .46
 1             0             0            -.46
 1             0             0             0
 1             0             0             .46
 1             0             0            -.46

ENERGY:  is the total energy of the given structure (Hartree) and it is present in the .MOL files containing the structure of a geometry optimization carried out by Gaussian-98 or CRYSTAL03. Together with this record, the FORCEMAX (maximum force), FORCERMS (root mean sqaure force), DISPLMAX (maximum displacement) and DISPLRMS (root mean square displacement) are reported as computed during the geometry optimization.

Example:

ENERGY        -232.263586392
FORCEMAX      0.000073
FORCERMS      0.000032
DISPLMAX      0.000101
DISPLRMS      0.000045

 

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