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

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Fri, 16 Jul 2004 18:36:22 -0400 (EDT)

Oliver,

I want to share my own experience with the RESP calculations. According to
the AMBER's procedure of optimizing the structure and getting the ESP data
points, the input gaussian file will have the following command:

#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt

I tried to recalculate the Cornell's RESP charges, published in 95. When I
used the above command in the gaussian input file, the charges I got were
pretty different than the Cornell's result. I did it for Cytosine. The
difference was something like 0.2.

When I followed the RED's procedure, the results were pretty close to the
Cornell's result. They use the following commands for optimization and
MEP calculation:

#P hf/6-31G* Opt=Tight SCF(Conver=8) Test ----> For optimization
(minimization procedure)

#P hf/6-31G* Pop=mk SCF(Conver=6) IOp(6/33=2) NoSymm Test ---> For MEP
calculation

Try RED to calculate the RESP.

Best,

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -                              -
  - University of Rochester      -                              -
  - Hutchison Hall, Office B10   - Ph.:(585) 503 44 00 (Cell)   -
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
  - http://www.pas.rochester.edu/~yildirim/                     -
  ---------------------------------------------------------------
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
>
>
>
>
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Received on Sat Jul 17 2004 - 00:53:00 PDT