There are several options in Antechamber to guess atom and bond types (using the -j flag). Some of these only work with certain charge methods, such as bcc will change prediction types <4 to 4 (but 5 will still work).
I have seen Antechamber "fail" with some charged species because of some of the atom/bond assignments. Since mol2 files contain bond types, these don't necessarily need to be guessed, so the option -j 5 has worked for me in these cases. This will still do partial bond type assignment, but should honor the mol2 bond types for the most part.
Reference for -j:
- 0: No judgement
- 1: Atom type
- 2: Full bond type
- 3: Partial bond type
- 4: Atom and full bond type
- 5: Atom and partial bond type
There are several options in Antechamber to guess atom and bond types (using the
-jflag). Some of these only work with certain charge methods, such asbccwill change prediction types <4 to 4 (but 5 will still work).I have seen Antechamber "fail" with some charged species because of some of the atom/bond assignments. Since mol2 files contain bond types, these don't necessarily need to be guessed, so the option
-j 5has worked for me in these cases. This will still do partial bond type assignment, but should honor the mol2 bond types for the most part.Reference for
-j: