Dear Junmei and others,
I am getting strange results when trying to parameterize some heterocyclic
cations using antechamber. Using a mol2 file for imidazole, when I do-
antechamber -i imidazole.mol2 -o imidazole_out.prepi -fi mol2 -fo prepi
I get a prep file for imidazole that has ring atom types cc, cd, and na.
But when I do the same thing for imidazolium, I get atom types c2 and na.
Because GAFF c2 is not aromatic, the dihedral parameters about the ring
become significantly weaker. The protonation should not affect the
aromaticity like this, correct? I see the same thing
for constitutively charged, n-substituted imidazoliums, as well as for
thiazoles vs thiazoliums.
Is this the correct antechamber / GAFF behavior? If so, why?
I've attached the input and output files.
Thanks,
Gabriel
Gabriel Rocklin
UCSF Shoichet/Dill Labs
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Received on Tue Feb 09 2010 - 00:00:03 PST
