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Partial Charges for Rare Atoms #1903
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Hi @maciejwisniewski-drugdiscovery, Unfortunately, we don't currently support loading/handling transition metals (which I believe is that issue causing the "radicals" error with the iron-containing compound in part 1), and even if we did, the AM1BCC charge method does not support the elements in your Cheers, |
Hi,
I'm working with a dataset containing SMILES strings of various ligands, and I want to calculate partial charges for each of them using either the Gasteiger or AM1BCC method.
Here is the Python code I'm using:
However, I've encountered a couple of issues:
1. Ligands with Radicals (?):
[S]12[Fe]3[S]4[Fe]1[S]1[Fe]2[S]3[Fe]41
SF4
Do you have any ideas how to omit that error?
2. Ligands with Atoms Lacking Parameters in Charge Calculation Methods:
List of Not Working Atoms in my DataSet
CCC1=C(C)C2=Cc3c(CC)c(C)c4n3[Rh@SP3]35n6c(c(C)c(CCC(=O)O)c6=CC6=[N+]3C(=C4)C(C)=C6CCC(=O)O)=CC1=[N+]25
SF4
Gasteigert
:am1-bcc
:array([nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan, nan,
nan]) <Unit('elementary_charge')>
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