Re: AMBER: Non-standard amino acid residue

From: FyD <>
Date: Mon, 16 Jul 2007 18:45:07 +0200

Quoting Sergey Samsonov <>:

> I'm trying to introduce non-standard amino acid residue into my protein
> for the further MD simulation. To accomplish that I get the parameters
> for -NH-CHR-CO- in ANTECHAMBER. Then I create the library for the
> residue and add it into the libraries in Xleap and so on. I realized
> that the charges for N, C, CA (and the other, of course, too) atoms in
> the prepin file are quite different (for a example for peptide bonded N
> with the calculated n1 type it is at least 0.2-0.3 charge units more
> negative than peptide bonded N in standard amino acid ) compared to
> standard amino acids. It is not a surprise since 1. AM1-BCC method for
> sure should give the results different from standard AMBER charges 2. N
> atom, for example, has one more uncoupled electron pair compared to the
> N atom in peptide-bonded state.

- For a same structure/conformation, the RESP charge value of an atom
available in the AMBER force field topology database present a charge
incertainty of 0.07 e. This is because of the orientational dependence
of RESP and ESP charge values.

- Then, here you compare charge values for different residues (no
information about their conformations !), and RESP vs AM1-BCC for
different structures/conformations: You get higher differences which
seem logical. I am not sure you can find empirical rules, and I am not
sure such comparisons mean something...

> Is there the way to use non-standard
> amino acid residues within the protein without this charge problem?

Electrostics is a key component of the FF energy.

Concerning RESP and ESP charges & non-standard residues you might wish
to have a look at the R.E.D. tutorial .
You will find information about multi-orientation, multi-conformation
and multi-molecule RESP fit for non-standard residues and their
fragments (central and terminal ones).

regards, Francois

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 18 2007 - 06:07:29 PDT
Custom Search