A follow up to my previous question - I noticed that rdkit and antechamber
give different results for some molecules, particularly on and around
nitrogens. Some of the minor differences (~1e-5) can be attributed to the
RMSD cutoff, which is not terrible, but also not adjustable without
recompiling.
What I finally realized is that the table in /dat/antechamber/GASPARM.DAT
has two extra entries for aromatic nitrogens with and without a formal
charge (unfortunately called "na" and "na+", respectively). These are not
in the original paper, nor the table in rdkit.
Does anyone know where these parameters came from?
Cheers,
Brian
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Received on Fri Dec 09 2022 - 08:30:02 PST
