The default behavior of the interface assumes that the end-user
strictly follows the interface rules. Namely, it is the user's
responsibility to provide a correct input file[*] with a number of
hydrogen atoms that is compatible with the specified charge on the
molecule (possibly defined using the last two digits in the filename).
N.B. : if the
user does not specify the total charge using the last two digits of
the filename, PrimaDORAC assumes no charge on the
The default behavior can be bypassed using the provided drop-down menu where
[*] There are many excellent freely accessible web applications to generate reliable 3D structures for drug size molecules. Effective 3D model generators can be found, for example, at the molinspiration site, the pubchem database, the Jacob Durrant's SMILES-to-3D visualizer or the chemozart web-based tool.