Re: [AMBER] obtain or build parameters for non-natural residues

From: Karl Kirschner <>
Date: Mon, 23 May 2016 09:31:24 +0200

Hello Aline,

  The model development of nonstandard residues is a difficult thing to do.
The main issues that one has to consider include a) determining partial
atomic charges that are balanced with your desired force field, b) are
there atom types that already exist in desired force field that can be used
to describe your molecule, or will you need to create new atom types c)
choosing the Lennard-Jones parameters for new atom types, d) parameterizing
any missing bond, angle, and torsion parameters using target experimental
and/or quantum data. Amber's antechamber program is a good place to start,
which can provide AM1-BCC charges easily and approximate missing
parameters. However, to truly optimize bonded parameter one needs to use
target experimental and/or QM data, which can be very time consuming since
you might need to generate QM potential energy curves of various internal
coordinates. The R.E.D. server is a good place for determining more robust
charges that are balanced with a given force field. The other thing to
consider is if these nonstandard residues will be used as part of the
primary sequence of a protein, or if they will be used a nonbonded ligands.
In the former case, one needs to make sure the charges and parameters are
balanced with the protein force field. In the later case, one has the
option of using the GAFF force field for modeling the ligand component.


On Fri, May 20, 2016 at 9:45 AM, ALINE THOMAS <> wrote:

> Dear Amber users and developers
> I am looking for .lib or .frcmod files for amber for two non-natural
> residues
> as gamma-carboxylic glutamic acid (GLA) and beta-hydroxy-aspartate
> residues (BHA),
> could not find anything on the archive, or from any website (PTM, NCAA,
> Bryce lab...)
> would you have any helping advice for obtaining them
> or for building them de novo ? never done that,
> Thank you very much for your help
> Aline
> --
> Aline Thomas, PhD
> Département de Pharmacochimie Moléculaire
> Université Joseph Fourier BP53
> 470, rue de la chimie
> 38041 Grenoble cedex 9
> Tél : +33 (0)
> Fax : +33 (0)
> _______________________________________________
> AMBER mailing list

Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
AMBER mailing list
Received on Mon May 23 2016 - 01:00:03 PDT
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