AMBER Archive (2004)

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

From: Rhonda Torres (torres_at_scripps.edu)
Date: Fri Jul 16 2004 - 16:20:42 CDT

Hi Oliver,

What total charge did you tell Antechamber to use to calculate for the
molecule? The AM1-BCC partial charges you provided add up to -0.22 while
the resp partial charges add up to -0.38.

Please include the output file for Antechamber.

Thanks,

Rhonda

On Fri, 16 Jul 2004, Oliver Hucke wrote:

> 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_at_u.washington.edu
> _______________________________________________________________
>
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