User 2466ec6b83
29-09-2006 14:49:28
The command to calculte is followed,
cxcalc -S -o sdf.txt input charge -t pi,total,sigma atompol
And the result is,
Marvin 09290615412D
2 1 0 0 0 0 999 V2000
-3.7813 0.7188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0668 1.1313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
M END
> <CHARGE>
0.00;0.00
-0.11;-0.11
-0.11;-0.11
> <ATOM_POLARIZABILITY>
1.36;1.36
$$$$
Only one tag of charge is in the result. If pi charge, total charge, and sigma charge have tag, individually, it should be better, especially for the people who read by program.
Such as
> <PI CHARGE>
0.00;0.00
> <TOTAL CHARGE>
-0.11;-0.11
> <SIGMA CHARGE>
-0.11;-0.11
Thanks,
User 2466ec6b83
30-09-2006 14:02:52
Same problem for orbital electronegativity
ChemAxon e08c317633
02-10-2006 12:22:39
Hi,
You can specify individual tags for the calculations with "-t" cxcalc option. (Note: there is a global cxcalc "-t" option to specify the name of the SDF tag, and usually there is a "-t" option for each calculation to set the type of the calculation. See
cxcalx help or cxcalc -h for more details.)
Example:
1. Calculate the pi charge and store the result in PI_CHARGE sdf tag:
| Code: |
| $ cxcalc -S -t PI_CHARGE -o output1.sdf input.sdf charge -t pi |
output1.sdf:
| Code: |
Marvin 10020613512D
6 6 0 0 0 0 999 V2000
0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
1 6 4 0 0 0 0
M END
> <PI_CHARGE>
0.00;0.00;0.00;0.00;0.00;0.00
$$$$
|
2. Calculate the total charge and store the result in TOTAL_CHARGE sdf tag:
| Code: |
| $ cxcalc -S -t TOTAL_CHARGE -o output2.sdf output1.sdf charge -t total |
Note: we use output1.sdf as input.
output2.sdf:
| Code: |
Marvin 10020613522D
6 6 0 0 0 0 999 V2000
0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
1 6 4 0 0 0 0
M END
> <PI_CHARGE>
0.00;0.00;0.00;0.00;0.00;0.00
> <TOTAL_CHARGE>
-0.06;-0.06;-0.06;-0.06;-0.06;-0.06
$$$$
|
3. Calculate the sigma charge and store the result in SIGMA_CHARGE sdf tag:
| Code: |
| $ cxcalc -S -t SIGMA_CHARGE -o output3.sdf output2.sdf charge -t sigma |
Note: we use output2.sdf as input.
output3.sdf:
| Code: |
Marvin 10020613522D
6 6 0 0 0 0 999 V2000
0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
1 6 4 0 0 0 0
M END
> <PI_CHARGE>
0.00;0.00;0.00;0.00;0.00;0.00
> <TOTAL_CHARGE>
-0.06;-0.06;-0.06;-0.06;-0.06;-0.06
> <SIGMA_CHARGE>
-0.06;-0.06;-0.06;-0.06;-0.06;-0.06
$$$$
|
Same solution works for orbital electronegativity.
Best regards,
Zsolt