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

From: David Case <>
Date: Thu, 19 Dec 2019 13:01:15 +0000

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 (?!?)


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Received on Thu Dec 19 2019 - 05:30:02 PST
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