Re: [AMBER] Attaching Methoxy (OMe) Capping at C-terminal

From: Pallab Dutta <>
Date: Thu, 19 Dec 2019 20:10:47 +0530

Dear David,

Thanks for your advice.
Although I see that capping with NME instead of OMe will not be very
Actually I am trying to reproduce an experimental observation, where such a
model peptide was used.
Hence I thought to remain strict on that.

Thank you again.

Pallab Dutta

On Thu, Dec 19, 2019 at 6:31 PM David Case <> wrote:

> On Thu, Dec 19, 2019, Pallab Dutta wrote:
> >
> >I am trying to make the following using tleap.
> >Ac-Xaa-OMe, where -
> >Ac is Acetyl group: -(C=O)-(CH3)
> >Xaa: any amino acid, for my case it is a Proline
> >OMe is methoxy group: -O-(CH3)
> >
> You will need to construct an "OME" unit as a capping group. I'd
> suggest starting with the existing NME group, and change N to O. You
> will then need to generate charges, and probably dihedral parameters for
> things the the CA-C-CT dihedral. Using gaff with Amber atom types would
> be a good place to start.
> Of course, maybe the fact that NME already exists might suggest a change
> in the capping group to be used (?!?)
> ....dac
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Received on Thu Dec 19 2019 - 07:00:02 PST
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