AMBER: RESP vs. AM1-BCC charges for isoprene

From: Oliver Hucke <>
Date: Fri, 16 Jul 2004 14:00:57 -0700

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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Received on Fri Jul 16 2004 - 22:53:00 PDT
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