AMBER Archive (2007)

Subject: Re: AMBER: Non-standard amino acid residue

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Jul 16 2007 - 11:45:07 CDT

Quoting Sergey Samsonov <sergeys_at_biotec.tu-dresden.de>:

> 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 @
http://q4md-forcefieldtools.org/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

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