| User keywords
In the following, the complete list of the allowed
keywords which can be specified in a MOL file is reported. The
meaning and a short example is also included. As a general rule,
the information to which any keyword refers is on a record
immediately following the keyword itself.
TITLE : any string not exceeding 70 characters.
Example:
TITLE
n-butane with standard
geometry
CELL : a, b, c axial lengths in angstroms
and alpha, beta, gamma angles
in degrees,
defining the crystallographic unit cell.
If the atomic positions are
expressed as orthogonal
cartesian coordinates, then this record should be 1 1 1 90 90 90. If
one of the axial lengths is negative, the program will not
display that particular axis, when the cell contents will be
generated (useful for displaying slices of planar
structures).
Example:
CELL
10.034
8.456 12.341 90.0 97.31
90.0
COORD : the atomic number and the three X, Y, Z
(fractional or cartesian in angstrom) coordinates are provided. A final
line containing all zero values is required to end the geometry input.
Example:
COORD
6 0.3456 0.9876 -.3334
6 0.1234 0.5678 -.7896
7 0.5631 -.3300 .2340
. ...... ...... .....
. ...... ...... .....
0 0
0 0
COORDAU : the atomic number and the three X, Y, Z
coordinates in atomic units (1 a.u.= 1 bohr = 0.5291771 Angstrom) are
provided. A final line containing all zero values is required to end
geometry input. This is useful to enter geometry as resulting from quantum
mechanical calculation (TURBOMOLE, CRYSTAL and GAMESS codes).
Example:
COORDAU
. ...... ...... .....
6 0.1234 0.5678 -.7896
7 0.5631 -.3300 .2340
. ...... ...... .....
. ...... ...... .....
0 0
0 0
COSYMB : the sequence number (even in random
order but without omissions), the atomic
symbol and the three X, Y, Z atomic coordinates
are supplied. A final line containing all zero values is required to
end geometry input. The atomic symbol is a string of characters; the
first two (one) characters are recognized as standard atomic
symbol, therefore the user must avoid ambiguous notations (for
instance do not indicate by HO3 an hydrogen atom attached to
oxygen O3, because the atom would then be recognized as an
holmium!). Spaces are not allowed within the atomic symbol string.
Example:
COSYMB
. . ......
....... .....
3 C
0.3456 -.1234 0.4554
5 N34 -.4444
1.2344 0.8999
7 C(12') 0.3456 -.1232
0.4545
9 N(1a) -.4444 1.2343
0.2343
10 HA3'
0.89 0.7346 1.234
. .
...... ...... .....
. .
...... ...... .....
0 0
0
0
0
MATZ: the geometry is given in terms of
internal coordinates (bond distances, bond angles and torsion angles). The
same format adopted in the AMPAC program (Dewar et al., JACS,1977,
99, 4899) is used. The atom type is specified by the atomic number.
Example: ethane molecule in staggered conformation, in which atoms 1,6,5,8,7
and 4 are hydrogens and 2 and 3 are carbons. Bonds are: 1-2, 2-6, 2-5,
2-3, 3-8, 3-7, 3-4.
1
8 in which 1-2-3-4
are
7 in the same
plane
2 ---- 3
6
5
4
MATZ
1 0.0
0 0.0 0 0.0
0 0 0 0
6 1.08 0
0.0 0 0.0 0 1
0 0
6 1.54 0
109.5 0 0.0 0 2
1 0
1 1.08 0
109.5 0 180.0 0 3 2 1
1 1.08 0
109.5 0 60.0 0 2 3
4
1 1.08 0
109.5 0 -60.0 0 2 3 4
1 1.08 0
109.5 0 60.0 0 3 2
1
1 1.08 0
109.5 0 -60.0 0 3 2 1
0 0
0 0 0
0 0 0 0
0
The first number is the atomic number followed by the bond length, the
bond angle and the torsion angle. The digit
after each geometrical parameter will not be used by MOLDRAW, and it is
given in order to keep compatibility with the AMPAC format.
The last three numbers are the sequential numbers of the atoms in
terms of which the preceding geometrical parameters definition is
possible. The forth line in MATZ indicates that hydrogen number 4 is
linked to carbon 3 with a bond length of 1.08 Angstrom, with
angle 4-3-2 of 109.5 degrees and torsion angle 4-3-2-1 of
180 degrees. The last line containing all zero values is required to end
geometry input. The algorithm used to transform from Z-matrix to
cartesian coordinates is such that the first four atoms should be in
the sequence 4-3-2-1. Any other starting sequence can cause unpredictable
results.
G94OUT: the geometry comes from the standard orientation of
a Gaussian-94 calculation and it is simply past after the keyword. The last
record contains all zero values to terminate the geometry specification.
Example:
TITLE
Example from G94 input
CELL
1 1 1 90 90 90
G94OUT
1
1
.934313 .911204
.000000
2
8
.000000 1.059921
.000000
3
14
-1.093175 -.091600
.000000
4
9
-2.509469 .557642
.000000
5
9
-.978110 -1.022611 1.252894
6
9
-.978110 -1.022611 -1.252894
7
6
3.407953 .330315
.663755
8
6
3.407953 .330315
-.663755
9
1
3.571874 1.232669 1.226370
10
1
3.261080 -.574538 1.227034
11
1
3.571874 1.232669 -1.226370
12
1
3.261080 -.574538 -1.227034
0
0
0
0 0
G98INP: the geometry is that contained in a .GJF or .COM
Gaussian-98 input files. The only supported format is that envisaging cartesian
coordinates. The last record contains all zero values to terminate the geometry
specification.
Example:
TITLE
Example from G98 input
CELL
1 1 1 90 90 90
G98INP
C 0 0.037920
1.202780 0.000000
C 0
1.437920 1.202780
0.000000
C 0 2.137920
-0.009656 0.000000
C 0
1.437920 -1.222092
0.000000
C 0 0.037920
-1.222092 0.000000
C 0
-0.662080 -0.009656
0.000000
H 0 -0.462080
2.068805 0.000000
H 0
1.937920 2.068805
0.000000
H 0 3.137920
-0.009656 0.000000
H 0
1.937920 -2.088117
0.000000
H 0 -0.462080
-2.088117 0.000000
H 0
-1.662080 -0.009656
0.000000
O 0 -4.162080
-0.009656 0.000000
H 0
-4.497260 0.450793
0.797522
H 0 -4.497260
0.450793 -0.797522
0 0
0
0
0
G98OUT: the geometry comes from the standard orientation of
a Gaussian-98 calculation and it is simply past after the keyword. The last
record contains all zero values to terminate the geometry specification.
Example:
TITLE
Example from G98 output
CELL
1 1 1 90 90 90
G98OUT
1
6
0 0.000000
1.420000 0.000000
2
6
0 1.229756
0.710000 0.000000
3
6
0 1.229756
-0.710000 0.000000
4
6
0 0.000000
-1.420000 0.000000
5
6
0 -1.229756
-0.710000 0.000000
6
6
0 -1.229756
0.710000 0.000000
7
1
0 0.000000
2.520000 0.000000
8
1
0 2.182384
1.260000 0.000000
9
1
0 2.182384
-1.260000 0.000000
10
1
0 0.000000
-2.520000 0.000000
11
1
0 -2.182384
-1.260000 0.000000
12
1
0 -2.182384
1.260000 0.000000
0
0
0
0
0 0
G98ARCH: the geometry comes from the file with extension
.RES under the TMP_P directory which MOLDRAW writes after reading the
Gaussian-98 optimization output (final convergence should be reached). The .RES
files contains the final optimized geometry with full numerical precision and it
is good to mantain the symmetry between subsequent manipulation. The last record
contains all zero values to terminate the geometry specification.
Example:
TITLE
Example from .RES g98 file
CELL
1 1 1 90 90 90
G98ARCH
C,0.6993926477,-1.2113835281,0.
C,1.3987852329,0.0000000361,0.
C,0.6993925852,1.2113835642,0.
C,-0.6993926477,1.2113835281,0.
C,-1.3987852329,-0.0000000361,0.
C,-0.6993925852,-1.2113835642,0.
H,1.2426359033,-2.1523083914,0.
H,2.4852716954,0.0000000642,0.
H,1.2426357921,2.1523084556,0.
H,-1.2426359033,2.1523083914,0.
H,-2.4852716954,-0.0000000642,0.
H,-1.2426357921,-2.1523084556,0.
0,0,0,0,0
CRY03OUT: the geometry comes from the output (.out) file of
a CRYSTAL03 run. MOLDRAW is natively able to read the CRYSTAL03 output file.
However, there are cases in which may be more handy to cut and paste a given
geometry during a long optimization run. The user should manually update the
cell parameters accordingly with those supplied in the CRYSTAL03 output file and
add the last record closing the input geometry.
Example:
TITLE
test from the crystal03 output of a polymer
system
CELL
6.48773283 1. 1. 90. 90.
90.
CRY03OUT
1 T 14 SI
6.572506976195E-05 1.891636048360E+00
0.000000000000E+00
2 F 14 SI
6.572506976195E-05 -1.891636048360E+00 0.000000000000E+00
3 T 8 O 2.367057529144E-01
1.344457896593E+00 0.000000000000E+00
4 F 8
O 2.367057529144E-01 -1.344457896593E+00
0.000000000000E+00
5 T 8 O
1.611796223536E-02 3.531040331793E+00
0.000000000000E+00
6 F 8 O
1.611796223536E-02 -3.531040331793E+00 0.000000000000E+00
7 T 14 SI -2.404037197442E-01 0.000000000000E+00
1.884881577395E+00
8 F 14 SI
-2.404037197442E-01 0.000000000000E+00 -1.884881577395E+00
9 T 14 SI 3.789112081407E-01
0.000000000000E+00 0.000000000000E+00
10 T 1
H -1.161711771452E-01 4.003362196364E+00
0.000000000000E+00
11 F 1 H
-1.161711771452E-01 -4.003362196364E+00 0.000000000000E+00
12
T 8 O -4.786811028450E-01
0.000000000000E+00 1.346199128645E+00
0 0 0 0 0 0 0
GROUP: define the
space group symbol. All 230 space group symbols are supported. The space group
list of the available symbols is stored in the ASCII file
GROUP.LST and the corresponding symmetry records in the GROUP.DAT file. The
user can add new space group symbols (to define non-standard
orientations) by updating the two files. It is recommended that both will
be backuped up before making any definite changes.
Example:
GROUP
P21/C
The list of groups contained in the GROUP.LST file is read by MOLDRAW at
startup. The space group specification for a given structure is made within
MOLDRAW by the
(Crystal--->Select space group...) menu.
Once the group symbol is selected from the space_group.lst file MOLDRAW reads the corresponding symmetry
records from the space_group.dat
file and the SYMNUM records are
appended to the .MOL file (see next keyword).
From that point on, the space group and symmetry records are permanently
stored in the .MOL file. If, for some reasons, the user needs to change them the
space group and symmetry records should be manually deleted from the .MOL
file.
SYMNUM: the components of the translation
vectors T and the elements of the rotation
matrices R are given. (ICSD files generated specifying
the symmetry record option are compatible with the
SYMNUM format). Each operator takes one record:
T1 T2 T3 R11 R12 R13 R21
R22 R33 R31 R32
R33
The last record is a line with T1=T2=T3=-1 and Rij=0.
Example:
SYMNUM
0. 0.
0. 1 0 0 0
1 0 0 0 1
0.5 0. 0.5 -1 0
0 0 1 0 0 0 -1
....................................................
-1. -1. -1. 0 0 0
0 0 0 0 0
0
SYMSIM: the symmetry operators are given following
the notation of the International Tables for X-Ray
Crystallography, Vol. I. Each symmetry operator requires one record
and the input is termi-nated by a record containing the END keyword.
Example:
SYMSIM
x,y,z
-x,1/2+y,1/2-z
-x,-y,-z
x,1/2-y,1/2+z
END
CHARGE: net atomic charges as resulting from a
previous quantum-mechanical calculation. Sequence numbers (even in random
order but without omission) and charge values are
required.
Example:
CHARGE
1 0.1234
2 -.2345
3 1.098
. .....
SCAN: to define a series of selected geometrical
degrees of freedom to be scanned through the SCAN command.
This option may only be used when the geometry is input via
the MATZ directive. The SCAN keyword requires the following records:
i) the number of degrees of freedom to be scanned; ii) for each
degree of freedom the number of the row of the Z-matrix where
it is defined, its type (bond, angle or torsion), the initial, the
final and the step values to be used in the scan and a reference user
defined label. For each point an energy evaluation is carried out and is
reported at the bottom of the screen, together with the new geometry. Three
files are also created, COULOMB.DAT, TOTALEN.DAT and VDWAALS.DAT
containing the value of the geometrical degree of freedom
being scanned and the corresponding value of the energy, partitioned as
pure electrostatic, total and non-bonded exp-6 contributions. This option
is useful to move monomers defining an hydrogen bond complex
in order to look at the most favorable
conformation. A complete example
follows:
Given the Z-matrix (atomic number 101 and
100 indicate lone pairs):
MATZ
101 0.00000 0
0.000 0 0.000 0 0
0 0
8 0.9423 0
0.000 0 0.000 0 1
0 0
6 1.39872 0 109.63
0 0.000 0 2 1 0
1 1.08191 0 107.32
0 180.000 0 3 2 1
1 1.0882 0 112.131
0 118.78 0 3 2 4
1 1.0882 0 112.131 0
-118.78 0 3 2 4
100 0.67136 0 121.35324 0 104.32801
0 2 3 1
100 0.67136 0 121.35324 0 -104.32801
0 2 3 1
99 1.0 0
90.000 0 0.000 0 1
2 3
8 2.01 r
90.000 a 175.600 t2 1 9 2
6 1.39872 0 112.82 b
-115.000 t1 10 1 9
1 1.08191 0 107.32
0 52.000 t4 11 10 1
1 1.0882 0 112.131
0 118.78 0 11 10 12
1 1.0882 0 112.131 0
-118.78 0 11 10 12
1 0.9423 0 109.630
0 180.000 0 10 11 12
100 0.67136 0 121.35324 0 104.32801
0 10 11 15
100 0.67136 0 121.35324 0 -104.32801
0 10 11 15
0 0.00000 0 0.000
0 0.000 0 0 0
0
the following SCAN records can be given:
SCAN
2
----> number of degrees to be scanned
12
3 0. 90. 5. T4
! !
! ! ! !
!
! ! ! ! -----> label of the degree
of freedom
! ! ! !
---------> increment
! !
! ------------> final value
! ! ----------------> initial
value
! -------------------> 1
(bond) 2 (angle) 3 (torsion)
----------------------> row of the Z-matrix
10 1 1.5
2.5 .1 R ---> row 10, bond, from 1.5 to
2.5
step 0.1 angstrom label R
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