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.
Oliver
=====================================
Details of what I did are given here:
AM1-BCC:
antechamber -fi pdb -i isopren.pdb -fo mol2 -o isopren.mol2 -c bcc
RESP:
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
Then:
antechamber -fi gout -i isopren.out -fo ac -o isopren.ac
espgen -i isopren.out -o isopren.esp
respgen -i isopren.ac -o isopren.respin1 -f resp1
respgen -i isopren.ac -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: ohucke.u.washington.edu
_______________________________________________________________
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Received on Fri Jul 16 2004 - 22:53:00 PDT
