Hi Nitzan,
you should try to modify the molecule conformation as little as possible
between the two calculations; see the example below.
rom rdkit import Chem
from rdkit.Chem import AllChem
test_ion1 = Chem.MolFromSmiles('COC(=O)C(c1c1)C1[NH2+]1')
test_ion1 = Chem.AddHs(tes
Dear rdkitters,
I am trying to use rdkit descriptors to investigate protonation of
molecules in the gas phase
while testing my procedure on Ritalin, I try to calculate the protonation
energy on different functional groups in the molecule
although my understanding tells me protonation should occur
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