I've recently discovered that several MOL files from MetaCyc have been printing out this error message:
"Some features of [#7+]~[Cl-] cannot be converted to smiles. Use the cxsmiles, smarts or cxsmarts format."
(this error message in particular pertains to NH4CL--I've attached the mol file).
The error message is the same for several other MOL files such as AQUACOBIIIALAMIN (again, attached)
To get this error message I'm running this command:
cxcalc -N hi majorms -H 7 AQUACOBIIIALAMIN.mol
Using MarvinBeans 5.11.1.
What could be the problem?