Dear all,
I encountered a problem with EmbedMultipleConfs which returns empty list for
some molecules (and for another molecules a few conformations when I don't add
Hs) I think both cases are linked since problems occur with high number of
rotatable bonds (more than 25). I tried to look for a solution but could only
find these old topics
https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/[email protected]/
https://sourceforge.net/p/rdkit/mailman/message/35698188/
which didn't help me so much, except it is a chirality problem almost for sure.
For example, EmbedMultipleConfs returns an empy list for this molecule.
smiles =
'CCCCCC1CCC(CC1)c2ccc(CCCCCOc3ccc4ccccc4c3c5c(OCCCCCc6ccc(cc6)C7CCC(CCCCC)CC7)ccc8cc(ccc58)N=Nc9ccc%10c(ccc(OCCCCCc%11ccc(cc%11)C%12CCC(CCCCC)CC%12)c%10c%13c(OCCCCCc%14ccc(cc%14)C%15CCC(CCCCC)CC%15)ccc%16ccccc%13%16)c9)cc2'
m = Chem.MolFromSmiles(smiles)
nr = int(AllChem.CalcNumRotatableBonds(m))
print("CalcNumRotatableBonds: ", nr)
m = Chem.AddHs(m)
ids = AllChem.EmbedMultipleConfs(m, numConfs=10, maxAttempts=500) # in my
tests, I choose numConfs at 500 at least,
print(len(ids))
Increasing numConfs help sometimes to find a few 3d conformations. Is it the
only solution due to the size of the number of rotatable bonds ?
Best regards,
Florian
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