Re: [AMBER] OMe fragment

From: Jason Swails <>
Date: Mon, 1 Mar 2010 20:55:45 -0500

On Mon, Mar 1, 2010 at 5:37 PM, Lekpa Duukori <> 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

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 M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Mon Mar 01 2010 - 18:00:03 PST
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