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
- Do nothing; Molecule is OK as is : Default behavior
- Check hydrogen atoms : Check using OpenBabel (ver 2.3.1) if hydrogen atoms are OK.
If test is passed, then the interface proceeds in generating the archive
- Add all hydrogen atoms : The molecule has only heavy
atoms or misses some hydrogen atoms. OpenBabel (ver 2.3.1) is used to
add all the missing hydrogen atoms and the resulting molecule is assumed
to be neutral.
- Add hydrogen atoms for pH=7: Add hydrogen atoms that are appropriate for
pH=7 (i.e. R-COOH --> R-COO- or R-NH2 --> R-NH3+ ). The resulting molecule can bear a net charge.
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.