Thanks Dr Case,
I dont think it will make a big diffrence as long as we can find the correct
charge for the atoms. I will treat them as (o).
David
On Wed, Jul 27, 2011 at 6:24 PM, David Case <dacase.rci.rutgers.edu> wrote:
>
>
> On Jul 27, 2011, at 4:19 PM, David Cantu <cantudav.amber.gmail.com>
>
> > I am manually assigning Gaff atom types.
> >
> > Would the oxygen in a deprotonotaed hydroxyl group (RO- instead of ROH)
> be
> > Gaff atom type (o) or (oh)?
>
> The "general" Amber force field is not (yet) general enough: the
> calibration/optimization never considered deprotonated alcohols. If it
> makes an important difference, one would probably need to define and
> parameterize new atom types.
>
> ...dac
>
> >
>
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Received on Thu Jul 28 2011 - 10:30:03 PDT
