Did you choose appropriate total charge of molecule (+1)?
Sincerely,
Dmitry Mukha
2010/2/9 Gabriel Rocklin <gabriel.rocklin.ucsf.edu>:
> 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 Wed Feb 10 2010 - 00:30:02 PST
