Re: When should I use NTER and NNEU as a patch?

From: Brian Radak (
Date: Wed Oct 12 2022 - 13:47:03 CDT

The answer, of course, depends on your system under study. It's fairly
common practice, at least for protein-ligand binding in globular proteins
to use the ACE and NME capping groups to avoid adding charges when large
gaps exist in a structure. This is preferable, in my opinion, than using
the neutral patches which may produce spurious h bond donor/acceptors.


On Wed, Oct 12, 2022, 1:50 PM Derman Basturk <> wrote:

> Dear NAMD Users,
> I previously posted this question in VMD mailing list but it is actually
> more related to the NAMD mailing list. I would appreciate any input.
> 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.
> Cheers.
> Derman

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