AMBER Archive (2004)

Subject: RE: AMBER: RESP vs. AM1-BCC charges for isoprene

Date: Thu Jul 22 2004 - 07:43:16 CDT

Hello Oliver,

AM1-BCC was NOT designed to reproduce RESP charges.

It does not make sense to design a charge model based on another charge
model. We designed the AM1-BCC model to reproduce the QM electrostatic
potential (ESP) at the HF/6-31G* level of theory. This is the same
fundamental idea behind RESP, however unlike RESP, AM1-BCC does not use HF
level of theory but rather the AM1 level to get a first approximation of the
QM ESP with the Coulson charges. These first-pass charges are then
corrected with bond-charge corrections (BCCs) in order to reproduce the QM

That said, I would not worry about large differences between AM1-BCC and
RESP for carbon atoms. It is well known that RESP charges suffer from
numerical instabilities, especially for buried atoms (i.e. charges can vary
widely while the RMS of the fit varies little). Table VI in the AM1-BCC
method paper shows this perfectly. Look at the RESP charges on Csp3 atoms,
they vary between -0.08 and +0.07, while for the same atoms the AM1-BCC
charges vary between +0.09 to +0.1.

Hope this helps,


Araz Jakalian, Ph.D.
Research Scientist, Structural Research Group
Boehringer Ingelheim (Canada) Ltd.
Research and Development
2100 Rue Cunard
Laval, Quebec, H7S 2G5, Canada
Phone: (450) 682-4640 Fax: (450) 682-4189

-----Original Message-----
From: Oliver Hucke [
<> ]
Sent: Friday, July 16, 2004 5:01 PM
Subject: AMBER: RESP vs. AM1-BCC charges for isoprene

Dear Amber users,

I have derived partial charges for an isoprene moiety with AM1-BCC and
with the resp procedure. I was surprised by the big differences of some
charge values - as you can see in this sketch:

        AM1-BCC RESP

     H3 0.04 H3 0.10
     | |
     C -0.06 H 0.11 C -0.36 H 0.09
      \ / \ /
-0.12 C=====C -0.17 0.2 C=====C -0.26
      / \ / \
     C C -0.06 C C -0.24
     | | | |
     H3 H3 0.04 H3 H3 0.09

Especially the carbons engaged in the double bond look suspicious to me
in the resp output (change of one charge from -0.12 with am1-bcc to 0.2
with resp). Might this be a resp fit artefact?

My understanding was is the AM1-BCC method was designed to reproduce the
RESP charges. So, I am wondering if something went wrong here.

Your comments are highly appreciated.


Details of what I did are given here:


antechamber -fi pdb -i isopren.pdb -fo mol2 -o isopren.mol2 -c bcc


1. Geometry optimization with gaussian98:
  # HF/6-31G* opt scf=tight test
2. ESP calculation:
  # HF/6-31G* pop=mk iop(6/33=2) iop(6/42=6) geom=check


antechamber -fi gout -i isopren.out -fo ac -o
espgen -i isopren.out -o isopren.esp
respgen -i -o isopren.respin1 -f resp1
respgen -i -o isopren.respin2 -f resp2
resp -O -i isopren.respin1 -o isopren.respout1 -e isopren.esp \
         -t iso.qout1
resp -O -i isopren.respin2 -o isopren.respout2 -e isopren.esp \
         -q iso.qout1 -t iso.qout2


Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: ____________________________________________________________

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