Thanks, but what I need is an OMe. I am modeling an experimental structure
that was actually capped with an OMe so I guess it's quite physical in this
case :)
Lepka
On Mon, Mar 1, 2010 at 7:02 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Mar 1, 2010 at 8:55 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > On Mon, Mar 1, 2010 at 5:37 PM, Lekpa Duukori <duukori.gmail.com> wrote:
> >> Dear AMBER users,
> >>
> >> Please does anyone know if there is an OMe fragment in the AMBER FF
> >> parameters? I want to do an OMe cap instread of the usial NMe
>
> Ah, misunderstanding. There is no O-Me. (i.e. COO-Me). The only caps
> are listed in my previous email, below.
>
> Sorry about that.
>
> >
> > There are three different "caps" allowed, two C-terminal caps and an
> > N-terminal cap. The two C-terminal caps are NME and NHE. NME is an
> > -NH-CH3 cap added to the end of the carbonyl of the last residue. NHE
> > is simply a -NH2. The N-terminal cap is ACE which is a CH3-CO- which
> > attaches to the nitrogen of the last residue (on the other side).
> > This seems to be the one you're looking for (since adding a carbonyl
> > to the C-terminus is silly and unphysical I would think, since there's
> > already a carbonyl there).
> >
> > Hope this helps,
> > Jason
> > --
> > ---------------------------------------
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> >
>
>
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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Received on Mon Mar 01 2010 - 18:30:04 PST
