AMBER Archive (2002)

Subject: Re: acetyl groups on protein fragments

From: Laurent Chiche (chiche_at_cbs.cnrs.fr)
Date: Fri Jul 26 2002 - 02:43:03 CDT

Hello,

I think it depends on what you actually want to simulate:

If you want to simulate a fragment "as if it was in the whole protein",
then it is usually best to protect the N- and C-termini (with acetyl
and amino groups) to avoid introducing charges where there is no
charge in the real protein.

If you want to simulate a fragment that has been (or will be
synthesized), then you should probably fit to what the fragment really
is or would be (i.e., protected or not protected).

Hope this helps
Laurent

Elizabeth K. White wrote:

> If I want to do MD simulation of a fragment of a protein, is there any
> reason I would perhaps want to add an acetyl group to the first amino
> acid?
>
> Thanks, E
>
>