Dear Gabriel,
If you look in the Amber force field topology database, you should
find the different FF libraries for various types of histidine (HIE,
HIS, HIP) with the corresponding FF atom types; you should see what FF
atom types you could use. Obviously, these FF atom types are in
capital & you want to use lower case FF atom types. But this could
give you some ideas...
regards, Francois
> 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 - 23:00:02 PST
