Re: [AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit

From: conor parks <>
Date: Wed, 4 May 2016 15:54:29 -0400

Thanks thomas,

I would like to clarify what you mean by smearing. If my net charge is
-0.001e, and I want to smear them onto the methyl hydrogens, am I correct
in assuming you mean subtract -0.001/3 from the charges on the methyl
hydrogens? Is there any way to determine if its better to smear onto the
methyl hydrogens or the HO hydrogen?


Conor Parks
B.S.E in Chemical Engineering, University of Michigan, 2012
PhD candidate in Chemical Engineering, Purdue University

On Wed, May 4, 2016 at 1:22 AM, Thomas Cheatham <> wrote:

> > I obtain a paracetemol molecule whos net charge is -0.001 e. This seems
> > large to me. I intend to simulate upwards of ~2500 paracetemol molecules,
> Round off error / finite precision happens. Try figuring a way to shift
> charge by hand slightly to make it net neutral. Although not absolutely
> necessary from a code/Ewald point of view since the methods can handle
> net-charge, from a reviewer's perspective, best to be neutral. I tend to
> look for a way to shift charges to hydrogens to get rid of the net charge.
> Tylenol? I would look to smear the charge on the methyl or the other
> terminal OH.
> > which would yield a net charge -2.5 e. I was wondering if someone could
> > comment on what would cause antechamber to not return a neutral molecule.
> Finite precision / round off.
> > My initial guess was perhaps the initial configuration was poor, but
> given
> No.
> --tec3
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Received on Wed May 04 2016 - 13:00:08 PDT
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