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 - 18:30:02 PST
