Hi,
I've got two questions:
1) am trying to convert smiles to 3D structures, using gen3D, but babel appears
to have issues with the stereochemistry:
example:
MDL mol file with desired stereo-chemistry, including 3D-coords and protons:
mol-beclomethasone_dipropionate.mol (included below)
prompt>
> In case it's working, how can I make use of it? I am now trying to compute
> energy of a periodic, crystalline structure, where I "manually" create bonds
> across the PBC, but this results in disaster. Removing the bonds across the
> PBC makes it better, but I have no clue whether it's because
