AMBER Archive (2004)

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

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Fri Jul 16 2004 - 17:49:00 CDT

Rhonda,

I should have mentioned that the two methyl groups connected to the same
sp2 carbon had identical (resp) and very similar (am1bcc) charges. I did
generally include only the charge of one of all equivalent atoms.
The overall charge is 0 in both cases.
(There was a small typo though. The charge of the highlighted hydrogen
is 0.14, not 0.09 as specified first. Sorry!)

           AM1-BCC RESP

        H3 0.04 H3 0.10
        | |
        C -0.06 H 0.11 C -0.36 H 0.14 <<<< former error
         \ / \ /
   -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

The attachment contains the mol2 output files for both molecules.

Thanks very much for your help!

OLiver

Rhonda Torres wrote:
> 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
_______________________________________________________________


@<TRIPOS>MOLECULE
MOL
   15 14 1 0 0
SMALL
rc

@<TRIPOS>ATOM
      1 C1 0.4410 -0.0420 -0.0000 c2 1 MOL 0.2008
      2 C2 -0.7280 -0.6650 -0.0000 c2 1 MOL -0.2627
      3 H1 2.3350 -0.5810 -0.8730 hc 1 MOL 0.1031
      4 C3 1.7340 -0.8250 0.0000 c3 1 MOL -0.3631
      5 H2 -0.7120 -1.7440 -0.0000 ha 1 MOL 0.1393
      6 H3 1.5580 -1.8950 -0.0000 hc 1 MOL 0.1031
      7 H4 1.2070 1.7610 0.8730 hc 1 MOL 0.1031
      8 H5 2.3340 -0.5820 0.8740 hc 1 MOL 0.1031
      9 C4 0.6350 1.4550 0.0000 c3 1 MOL -0.3631
     10 H6 -2.6680 -0.4100 -0.8730 hc 1 MOL 0.0897
     11 H7 -2.6680 -0.4090 0.8730 hc 1 MOL 0.0897
     12 H8 1.2070 1.7610 -0.8730 hc 1 MOL 0.1031
     13 H9 -0.2920 2.0090 -0.0000 hc 1 MOL 0.1031
     14 C5 -2.1130 -0.0750 0.0000 c3 1 MOL -0.2394
     15 H10 -2.1190 1.0060 -0.0000 hc 1 MOL 0.0897
@<TRIPOS>BOND
     1 1 2 2
     2 1 4 1
     3 1 9 1
     4 2 5 1
     5 2 14 1
     6 3 4 1
     7 4 6 1
     8 4 8 1
     9 7 9 1
    10 9 12 1
    11 9 13 1
    12 10 14 1
    13 11 14 1
    14 14 15 1
@<TRIPOS>SUBSTRUCTURE
     1 MOL 1 TEMP 0 **** **** 0 ROOT


@<TRIPOS>MOLECULE
MOL
   15 14 1 0 0
SMALL
bcc

@<TRIPOS>ATOM
      1 C1 0.4410 -0.0420 -0.0000 c2 1 MOL -0.1205
      2 C2 -0.7280 -0.6650 -0.0000 c2 1 MOL -0.1735
      3 H1 2.3350 -0.5810 -0.8730 hc 1 MOL 0.0402
      4 C3 1.7340 -0.8250 0.0000 c3 1 MOL -0.0604
      5 H2 -0.7120 -1.7440 -0.0000 ha 1 MOL 0.1149
      6 H3 1.5580 -1.8950 -0.0000 hc 1 MOL 0.0371
      7 H4 1.2070 1.7610 0.8730 hc 1 MOL 0.0406
      8 H5 2.3340 -0.5820 0.8740 hc 1 MOL 0.0402
      9 C4 0.6350 1.4550 0.0000 c3 1 MOL -0.0579
     10 H6 -2.6680 -0.4100 -0.8730 hc 1 MOL 0.0405
     11 H7 -2.6680 -0.4090 0.8730 hc 1 MOL 0.0405
     12 H8 1.2070 1.7610 -0.8730 hc 1 MOL 0.0406
     13 H9 -0.2920 2.0090 -0.0000 hc 1 MOL 0.0396
     14 C5 -2.1130 -0.0750 0.0000 c3 1 MOL -0.0599
     15 H10 -2.1190 1.0060 -0.0000 hc 1 MOL 0.0379
@<TRIPOS>BOND
     1 1 2 2
     2 1 4 1
     3 1 9 1
     4 2 5 1
     5 2 14 1
     6 3 4 1
     7 4 6 1
     8 4 8 1
     9 7 9 1
    10 9 12 1
    11 9 13 1
    12 10 14 1
    13 11 14 1
    14 14 15 1
@<TRIPOS>SUBSTRUCTURE
     1 MOL 1 TEMP 0 **** **** 0 ROOT

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