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

From: Bill Ross <>
Date: Wed, 4 May 2016 13:06:33 -0700

With methyl hydrogens you have chemical equivalence since they spin,
plus they are relatively neutral, whereas with HO you are localizing
your error to a charged, unique atom.


On 5/4/16 12:54 PM, conor parks wrote:
> 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?
> Regards,
> 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 - 13:30:03 PDT
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