Dear community,
I just found out that adding hydrogens to hydrochloride to later embed it and
use MMFF force field results on a force field that is not set up (convergency =
-1):
m = Chem.MolFromSmiles('Cc1ccccc1NC(=O)Cl.Cl')
m = Chem.AddHs(m)
AllChem.EmbedMultipleConfs(m, numConfs=5, useRandomCoords=True, randomSeed=43,
maxAttempts=5000)
res1 = AllChem.MMFFOptimizeMoleculeConfs(m, ignoreInterfragInteractions= False)
print(res1)
On the other hand, if hydrogens are already provided in the smiles (without
having to add hydrogens) works. I think this is a bug since it does not happen
with other simple molecules such as water.
m2 =
Chem.MolFromSmiles('[H]Cl.[H]c1c([H])c([H])c(C([H])([H])[H])c(N([H])C(=O)Cl)c1[H]')
AllChem.EmbedMultipleConfs(m2, numConfs=5, useRandomCoords=True, randomSeed=43,
maxAttempts=5000)
res2 = AllChem.MMFFOptimizeMoleculeConfs(m2, ignoreInterfragInteractions= False)
print(res2)
One way of solving this is by 1) getting the mol from smiles without hydrogens,
2) adding hydrogens to the mol, 3) going back to smiles (now with hydrogens),
4) getting a mol from smiles with hydrogens. It works, but it should not be
solved like that.
m3= Chem.MolFromSmiles('Cc1ccccc1NC(=O)Cl.Cl')
m3= Chem.AddHs(m3)
m3 = Chem.MolToSmiles(m3)
print("now it has Hs", m3)
m3= Chem.MolFromSmiles(m3)
AllChem.EmbedMultipleConfs(m3, numConfs=5, useRandomCoords=True, randomSeed=43,
maxAttempts=5000)
res3 = AllChem.MMFFOptimizeMoleculeConfs(m3, ignoreInterfragInteractions= False)
print(res3)
Is there some other place to report this kind of stuff?
Best regards,
Pablo Ramos
Ph.D. at Covestro Deutschland AG
[cid:image001.png@01D77801.4B425DE0]
covestro.com<http://www.covestro.com/>
Telephone
+49 214 6009 7356
Covestro Deutschland AG
COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD
B103, R164
51365 Leverkusen, Germany
pablo.ra...@covestro.com<mailto:pablo.ra...@covestro.com>
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