Re: [AMBER] Acetylated the truncated N- terminal

From: David Sáez <>
Date: Fri, 10 Apr 2020 01:02:24 -0400

Hi Lod,

I guess that piece of text refers to the charge derivation procedure for
residues that would normally be part of a bigger molecule or polymer.

For example, in deriving RESP charges for an aminoacid residue you cannot
use the zwitterionic or neutral molecule, because in an actual protein
that residue has "lost" some of the atoms in the formation of the peptide
bond. So the standard is, for charge calculation purposes,
to block the residue with NME and ACE residues at the C-terminal and
N-terminal groups, respectively. In that way I think you give a common
"peptide-like" environment to all your residues.

Then you make the QM calculations on that blocked structure, and in the
charge derivation process you keep the charges fixed to a standard value
for those blocking groups,
varying only the atomic charges of your actual residue.

The procedure is nicely explained in this tutorial,, for a
non-protein molecule.



On Thu, Apr 9, 2020 at 11:47 PM Lod King <> wrote:

> Hi Amber
> *I have seen many papers talking about *"acetylated the truncated N-
> terminal ....... to eliminate artificial charges at the N-termini"
> *I wonder what does it mean to the PDB structure and how did it achieve? *
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Received on Thu Apr 09 2020 - 22:30:02 PDT
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