I believe if you shift the Na and Cl atom names one step to the left, (column
14 to 13), andinsert a space after the atom name, as in:
from:
123456789012345678901234567890123456789012345678901234567890
ATOM 1 Na Na 1 0.000 0.000 0.000 1.00 0.00 NaATOM
2 Cl
hi,
using OB I've encountered some rather unexpected behavior whentrying to use the
--canonical flag: If I apply the babel (or obabel) command with the --canonical
flag repeatedly to the same structure I get different results
e.g., if i start with a molecule can-gefitinib.xyz a small molecule
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>
