VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Wed Oct 12 2022 - 01:38:40 CDT

Personally if I'm using a truncated model, I acetylate the N-Terminus
(CA-NH2 -> CA-NH-COMe) and methylamidate the C-terminus (CA-CO2H ->
CA-CONHMe).

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Wed, 12 Oct 2022 at 17:48, Derman Baştürk <drmnbastrk_at_gmail.com> wrote:

> Dear NAMD Users,
>
> My understanding is that when I have a full-length protein structure then
> I should use NTER and CTER as patches in the N and C terminus, except
> special cases when you have proline or glycine at the terminals. But what
> should I use if I do not have a full-length protein? Should I use the
> regular NTER or the neutral NNEU? I am asking because if I use NTER, I
> would be placing a positive charge at a location that would normally not be
> there. I couldn't find any detailed info on this. Any suggestion or reading
> material on this would be appreciated.
>
> Best regards.
>
> Derman
>