I believe this to be a bug with Avogadro
Environment Information
Avogadro version: 1.2
Operating system and version: Windows 10, 21H1
Expected Behavior
Output a .mol2 file with charges. See boron-less molecule below:
@MOLECULE
17 17 0 0 0
SMALL
GASTEIGER
@ATOM
1 C -1.3306 -10.2767 -0.0190 C.ar 1 UNL1111111 -0.0613
2 C -1.9055 -11.5458 0.0109 C.ar 1 UNL1111111 -0.0617
3 C 0.0728 -10.1779 -0.0598 C.ar 1 UNL1111111 -0.0538
4 C 0.9170 -11.3193 -0.0702 C.ar 1 UNL1111111 0.0075
5 C 0.2871 -12.6164 -0.0406 C.ar 1 UNL1111111 -0.0538
6 C -1.1117 -12.6837 -0.0003 C.ar 1 UNL1111111 -0.0613
7 C 2.4863 -10.9500 -0.1168 C.3 1 UNL1111111 0.1801
8 O 2.8822 -9.5417 -0.1824 O.3 1 UNL1111111 -0.3634
9 O 3.5703 -11.9182 -0.0942 O.3 1 UNL1111111 -0.3634
10 H -2.9823 -11.6635 0.0423 H 1 UNL111 0.0618
11 H 0.5160 -9.1969 -0.0825 H 1 UNL111 0.0622
12 H -1.6002 -13.6510 0.0217 H 1 UNL111 0.0618
13 H 3.0053 -9.2698 0.7623 H 1 UNL111 0.2128
14 H 3.9295 -11.8699 0.8281 H 1 UNL111 0.2128
15 H 1.9056 -11.8487 -0.1110 H 1 UNL111 0.0960
16 H -1.9198 -9.4295 -0.0114 H 1 UNL1 0.0618
17 H 0.8554 -13.4778 -0.0489 H 1 UNL1 0.0622
@BOND
1 2 1 ar
2 1 3 ar
3 4 3 ar
4 5 4 ar
5 5 6 ar
6 2 6 ar
7 4 7 1
8 7 8 1
9 7 9 1
10 2 10 1
11 3 11 1
12 6 12 1
13 8 13 1
14 9 14 1
15 7 15 1
16 1 16 1
17 5 17 1
Actual Behavior
Outputs a .mol2 file without charges. See same molecule as above, but with Boron:
@MOLECULE
16 16 0 0 0
SMALL
GASTEIGER
@ATOM
1 C -1.3306 -10.2767 -0.0190 C.ar 1 UNL11111111 0.0000
2 C -1.9055 -11.5458 0.0109 C.ar 1 UNL11111111 0.0000
3 C 0.0728 -10.1779 -0.0598 C.ar 1 UNL11111111 0.0000
4 C 0.9170 -11.3193 -0.0702 C.ar 1 UNL11111111 0.0000
5 C 0.2871 -12.6164 -0.0406 C.ar 1 UNL11111111 0.0000
6 C -1.1117 -12.6837 -0.0003 C.ar 1 UNL11111111 0.0000
7 B 2.4863 -10.9500 -0.1168 B 1 UNL11111111 0.0000
8 O 2.8822 -9.5417 -0.1824 O.3 1 UNL11111111 0.0000
9 O 3.5703 -11.9182 -0.0942 O.3 1 UNL11111111 0.0000
10 H -2.9823 -11.6635 0.0423 H 1 UNL1111 0.0000
11 H 0.5160 -9.1969 -0.0825 H 1 UNL1111 0.0000
12 H -1.6002 -13.6510 0.0217 H 1 UNL1111 0.0000
13 H 3.0053 -9.2698 0.7623 H 1 UNL1111 0.0000
14 H 3.9295 -11.8699 0.8281 H 1 UNL1111 0.0000
15 H -1.9198 -9.4295 -0.0114 H 1 UNL11 0.0000
16 H 0.8554 -13.4778 -0.0489 H 1 UNL11 0.0000
@BOND
1 2 1 ar
2 1 3 ar
3 4 3 ar
4 5 4 ar
5 5 6 ar
6 2 6 ar
7 4 7 1
8 7 8 1
9 7 9 1
10 2 10 1
11 3 11 1
12 6 12 1
13 8 13 1
14 9 14 1
15 1 15 1
16 5 16 1
Steps to Reproduce
Create an organic molecule with Boron in it and write it out as a mol2 file. I have also tried writing it as a pdb file.