Fully halogenated molecules cannot be generated

[rcruzsilva]

• [x] I believe this to be a bug with LigParGen

Issue Information

Software name & Version : LigParGen online Generator Method: FF generation by SMILE input of fully halogenated molecules.

Expected Behavior

I used the smiles input to generate CHF3 and CF4, as well as trichloromethane and carbon tetrachloride. The respective smiles are: FC(F)F, FC(F)(F)F, ClC(Cl)Cl, and ClC(Cl)(Cl)Cl. I also tried some bigger and more complex fluorinated molecules, with and without charges. Interestingly, as long as the molecules have at least one hydrogen, the molecule can be processed succesfully. See for instance this molecule, with -1 charge, there is no problem.
2,2,3-trifluoro-3-[1,1,2,2,3,3-hexafluoro-3-(trifluoromethoxy)propoxy]propanoate: C(C(C(=O)[O-])(F)F)(OC(C(C(OC(F)(F)F)(F)F)(F)F)(F)F)F

I am using the CM1A charge model, but I can see the problem occurs in both charge models.

Actual Behavior

Molecules CF4 and CCl4 failed during processing. CHF3 and CHCl3 were processed without any problem. For some reason fully halogenated molecules, even the simplest ones cannot be processed.