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

From: Thomas Cheatham <>
Date: Tue, 3 May 2016 23:22:09 -0600 (MDT)

> 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



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Received on Tue May 03 2016 - 22:30:03 PDT
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