On Mon, Mar 1, 2010 at 9:08 PM, Lekpa Duukori <duukori.gmail.com> wrote:
> 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 :)
Oh this certainly is. What I was referring to was capping the
C-terminus with a C=O-Me, so you'd be left with a C=O-C=O-Me which was
the target of my "unphysical" comment (which, if you could actually
apply an ACE to a C-terminus, is what you'd have, though the
connectivity in LEaP doesn't even allow this as far as I know).
Again, a rather silly misunderstanding of what you were asking for.
Though Lachele has pointed out that GLYCAM does have a C=OMe. She
gives good advice about creating a fragment for your needs.
Good luck!
Jason
>
> 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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>>
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--
---------------------------------------
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 - 19:30:03 PST
