It may be useful to do the QM calculation in this case with an implicit solvent model. The AMBER ff03 force field has been parameterised in this way.
________________________________________
From: Karl Kirschner [k.n.kirschner.gmail.com]
Sent: 01 February 2015 15:13
To: AMBER Mailing List
Subject: Re: [AMBER] Constructing a single Zwitterion in xleap
Hello,
Zwitterion are somewhat difficult to parametrize IMO. One complicating
fact is finding a set of observables that can be used for optimizing the
parameters. In the gas phase, zwitterions, whose "formal" charge separated
functionalities (i.e. -NH3+, -CO2-) are in close spatial proximity, are
unstable. Computationally, using an appropriate QM theory level results in
the hydrogen atom migrating back to the carboxylate group. Some QM theory
will incorrectly model the zwitterion as a stable species. (If memory
servers me, for glycine zwitterion it takes one or two explicit waters that
bridge the charge groups to create a stable gas-phase species.) This makes
computing a molecular electrostatic potential difficult to do or
questionable if obtained, and thus difficult to fit partial atomic charges.
One can make approximations by performing QM on the separate chemical
species and then assuming they are transferable to the zwitterion. (We did
this a long time ago for MM3.) However, this approach likely introduces
some error into modeling since their are significant quantum effects (e.g.
polarization) that occur when such chemical functionalities are in close
proximity. I think there has been some work on doing implicit QM modeling
of zwiterions, and might be worth doing a literature search on.
Best regards,
Karl
On Sun, Feb 1, 2015 at 1:55 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Feb 1, 2015, at 12:36 AM, Robert Molt <rwmolt07.gmail.com> wrote:
> >
> > I do beg pardon if this answer is obvious; I could not discern this from
> > the AmberTools manual.
> >
> > Is it possible, in using the xleap interface, to construct a sequence
> > composed of a single amino acid in zwitterion form? It's clear how to
> > make zwitterions for two or more amino acids, but I have an unusual
> > purpose for which I need a single amino acid zwitterion..
> >
> > If this is not an option, can one advise how one might construct a
> > zwitterion form in an easily recognizable for the prmtop file?
>
> Amber does not have any zwitterionic residue definitions in the available
> library files -- you will need to create your own residue library (e.g.,
> using antechamber) to derive the charges and connectivity. It’s really no
> different than parametrizing an arbitrary organic ligand.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
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Received on Sun Feb 01 2015 - 08:00:02 PST
