MOLDRAW: a program to display and manipulate molecular and crystalline structures

 

by Piero UGLIENGO  University of Torino - Dipartimento Chimica. Via P. Giuria 7 -10125 Torino. ITALY

MS Windows (Linux & Mac OS X) - 
http://www.moldraw.unito.it  

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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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