Dear Jim,
you can do that quite conveniently using antechamber from the AmberTools
<http://ambermd.org/AmberTools.php> package.
antechamber takes as input formats PDB, MOL2 and MOL, so it should be
pretty straightforward for you to interface it with the RDKit.
Please feel free to get back to me off-list if you get into trouble.
Cheers,
p.
On 03/11/19 18:55, James T. Metz via Rdkit-discuss wrote:
RDkit Discussion Group,
I am interested in generating and assigning AM1-BCC charges to
small molecules,
preferably in batch mode. I understand this topic has been discussed
previously, but
has there been RDkit code written to do this? Since this relies on
the results of AM1
calculations, has anyone perhaps written RDkit code to calculate and
assign the
charges if I have already generated a MOPAC output file by some other
means?
I greatly appreciate all the capabilities of RDkit, and not to be
off-topic, but if
someone is aware of a non-RDkit way to generate AM1-BCC charges, that
might work
for me. Hence, please let me know. Thank you.
Regards,
Jim Metz
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