Antechamber does not recognize boron, so we'll need to enter in the parameters ourselves. Our reference paper contains charges for each atom, so we'll use these numbers.

Type in:

Using your preferred text editor (e.g., vim or gedit), open bf4.mol2. We'll need to make few changes:

First, if the second digit in the third line of the file is a “0,” change it to 4. This means that our molecule will have four bonds (four fluorines bonded to boron).

Second, locate the last column in the “Atoms” category. These numbers represent each atom's charge. As of now, they're all zeros since we didn't identify a charge model. Correct the charges by replacing this column with the numbers provided in the paper. (Boron: 1.1504, Fluorine: -0.5376).

Finally, we'll need to add in the bonds manually. Bonds are specified by the bond id, two atom numbers (the first column in the atom section), and the bond type (1 for single bond, 2 for double bond, etc.)

Add a record under the “Bonds” category:

This would be the first record (the first number) that says that the B1 atom (the second number) and the F2 atom (the third number) will form a single bond (the fourth number).

Add three more records:

Note: Bond ids are all 1's, as the bond ids are of no significance in this case.