Hi Aron,
Thanks for the suggestion. That carbon surrounded by 3 nitrogen atoms is of
type CA, sp2 C pure aromatic (benzene), kind of counter-intuitive.
But I guess you have to look into the antechamber-generated atom types
anyway (as it would treat the two oxygen atoms in carboxylate group
differently). So I'd like to try to manually set all parameters.
Thanks,
Yun
On Tue, Oct 16, 2012 at 3:21 PM, Aron Broom <broomsday.gmail.com> wrote:
> I don't know what the answer should be, but, as something to add to your
> already having considered the PHE carbon, what about in ARG, the terminal
> carbon on the sidechain? It is also sp2 hybridized forming a planar group
> with its 3 attached heavy atoms, where two of the heavy atoms (the terminal
> nitrogens) can be double-bonded as in your ring, and other nitrogen (the
> one further back along the sidechain) also has a single hydrogen and is
> then bonded to a carbon.
>
> Having said that, isn't GAFF and antechamber supposed to have very generic
> types that could handle this? I wouldn't think you'd want to build this
> from atom types used for amino acids.
>
> ~Aron
>
> On Tue, Oct 16, 2012 at 3:39 PM, Yun Shi <yunshi09.gmail.com> wrote:
>
> > Hi everyone,
> >
> > What should be the atom type the the [1] carbon (an aromatic carbon
> > attached by amide nitrogen) in the picture if parm99.dat is used?
> >
> > I understand similar carbon atom in PHE (the aromatic one attached by
> -OH)
> > is of atom type C (sp2 C carbonyl group), but my molecule seems
> different.
> >
> > Thanks for any suggestion,
> >
> > Yun
> >
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>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Tue Oct 16 2012 - 16:30:03 PDT
