AMBER Archive (2009)

Subject: [AMBER] antechamber am1-bcc issues

From: David Mobley (
Date: Fri Aug 07 2009 - 13:19:53 CDT


I keep having issues with partial charges coming from Antechamber AM1-
BCC. In addition to the bug I mentioned previously relating to the -j
option resulting in incorrect charges when it should have no effect,
I'm also consistently finding that Antechamber generates substantially
different "AM1-BCC" partial charges than other implementations of AM1-
BCC. For a set of roughly 20 molecules, I obtained partial charges
from Christopher Bayly that he computed with his own, internal Merck
AM1-BCC implementation, and I also computed them with OpenEye's
Quacpac python toolkit. We then computed mean differences between
these charge sets. The Bayly AM1-BCC and OpenEye AM1-BCC
implementations agree extremely well, but Antechamber AM1-BCC charges
disagree with both Bayly and OpenEye partial charges reasonably

The differences are nontrivial -- they can make up to several kcal/mol
difference in computed hydration or binding free energies.

I am attaching just one example of profound disagreement. The 2-
nitrothiophene.mol2 file contains Bayly AM1-BCC partial charges (sybyl
atom naming); 2-nitrothiophene_ante_amber.mol2 contains antechamber
AM1-BCC partial charges (amber atom naming), and 2-
nitrothiophene_oechem_amber.mol2 contains OpenEye AM1-BCC partial

In this example, the Antechamber AM1-BCC charges differ from the
others by more than 0.3 e on the nitrogen alone.

Anyway, I just wanted to put this out there to advise people. It
appears I will be ditching the Antechamber AM1-BCC implementation
until some of these problems are straightened out.

David Mobley, Ph.D.
Assistant Professor of Chemistry
University of New Orleans
New Orleans, LA 70148
Phone 504-383-3662
Fax 504-280-6860

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