Hi Jérémie,
The partial atomic charges are a 100% artificial construct - there is no
quantum observable for them. Normally, to validate a charge set (and their
atom type's corresponding Lennard-Jones parameters) one has to do a
condense-phase simulation and compare to it's observables to experimental
values (e.g. density, enthalpy of vaporization). For your molecule, I am
not sure that is possible, but it might be worth looking into.
Based on my experience, both the resp and the am1-bcc look like
reasonable solution. If you plan to model this molecule in the presence of
other molecules that use existing AMBER force fields, then it is important
to ensure that the charges are balanced with that force field. That means,
they should be created using a methodology that is compatible with that
force field. For example, the partial atomic charges for AMBER protein
residue (which are modeled with Parm14SB), were generated using a 2-stage
resp approach (with weights 0.0005 and 0.001) that fit the MEP computed at
HF/6-31G(d) theory level. Glycam06 uses a similar approach but set all
aliphatic hydrogens to zero.
AM1-BCC is often used by this community to more easily supply partial
atomic charges. I "believe" it is often assumed that they are compatible
with the exiting charge set within AMBER's residue database. Perhaps
someone else can better comment on the use of AM1-BCC charge set with the
existing AMBER force fields.
If you need to ensure that the partial atomic charges are balanced with
an existing force field, I can help you out with that - just contact me
privately. Hope this helps some.
Cheers,
Karl
--
Karl. N. Kirschner, Ph.D.
Research Associate
Bonn-Rhein-Sieg University of Applied Sciences
Grantham-Allee 20, 54757 Sankt Augustin, Germany
On Tue, Oct 27, 2015 at 9:38 AM, Jérémie Knoops <jeremie.knoops.gmail.com>
wrote:
> Dear Amber users,
>
> I'm trying to determine the charges for phenylguanidinium.
> I normally use the RED servers (and very often multiconfigurational fit)
> but the q4md website is still down.
> Using RESP and Gaussian with one conformation (minimized structure), I get
> too high absolute values for them (up to 1.1 for a carbon atom,
> see GdPhenyl_resp.mol2).
> It's impossible to parametrize the molecule with those charges, the
> equilibrium bond length is 0.06 Å shorter than the reference bond length.
>
> I tried the am1-bcc scheme, also with one conformation and the charges
> seem reliable (see GdPhenyl_am1-bcc.mol2). I can parametrize the torsion
> with them.
> Do I have to use the am1-bcc charges? Are they really reliable? Are there
> other options?
>
> Thank you for your advice.
>
> *Jérémie Knoops*
>
> *PhD StudentLaboratory for Chemistry of Novel Materials
> <http://morris.umh.ac.be/default.aspx>*
> *University of Mons* <http://portail.umons.ac.be/en2/>
>
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Received on Tue Oct 27 2015 - 03:00:03 PDT
