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 molecule.

The default behavior can be bypassed using the provided drop-down menu where

N.B.: OpenBabel preprocessing on end-user files is not guaranteed to be foolproof . The user is thus encouraged to carefully prepare its own input file to be processed by the interface using the default behaviour.

Got it! Back to the interface

[*] 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.