Partial Charges MOPAC x Avogadro

General Discussion
1

Hi everybody

I’ḿ generating some ESPs from models minimized by MOPAC2009. The ESP for
Fenol and Fenolate looks strange… or may be wrong… When I active the
option “labels” - with partial charges, Avogadro returns me some partial
charges different from the MOPAC2009 calculated in Gabedit. So Avogadro is
not using the correct charges to produce the ESP… what should I do ?

Tks a lot !

Fernando Bachega

2

I’ḿ generating some ESPs from models minimized by MOPAC2009. The ESP for Fenol and Fenolate looks strange… or may be wrong… When I active the option “labels” - with partial charges, Avogadro returns me some partial charges different from the MOPAC2009 calculated in Gabedit. So Avogadro is not using the correct charges to produce the ESP… what should I do ?

Can you send me the file? The MOPAC files I’ve seen only have one set of charges. So I’d be interested to see the actual text.

Thanks,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

3

Geoffrey Hutchison

I’ḿ generating some ESPs from models minimized by MOPAC2009. The ESP for
Fenol and Fenolate looks strange… or may be wrong… When I active the
option “labels” - with partial charges, Avogadro returns me some partial
charges different from the MOPAC2009 calculated in Gabedit. So Avogadro is
not using the correct charges to produce the ESP… what should I do ?

Can you send me the file? The MOPAC files I’ve seen only have one set of
charges. So I’d be interested to see the actual text.

Geoffrey, Hi, I’ m paris now, and the original files are in brazil, But I’
m gonna try to reproduce the “errors” and send to you as soon as possible.

See Y

And really thanks

Thanks,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

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4

Here is the charges calculated by mopac using PM6 – whole information in
file phenolate.out

ATOM NO. TYPE CHARGE No. of ELECS. s-Pop p-Pop

1 H 0.144332 0.8557 0.85567
2 H 0.072378 0.9276 0.92762
3 C -0.581772 4.5818 1.12059 3.46118
4 C 0.063177 3.9368 1.09213 2.84470
5 O -0.692840 6.6928 1.72370 4.96914
6 C 0.671114 3.3289 0.99486 2.33402
7 C -0.491265 4.4913 1.08468 3.40658
8 H 0.117548 0.8825 0.88245
9 C -0.583969 4.5840 1.12025 3.46372
10 C 0.064515 3.9355 1.09218 2.84331
11 H 0.144578 0.8554 0.85542
12 H 0.072204 0.9278 0.92780

The picture show the partical charges which avogadro shows… and they are
the same as if I draw the phenolate (without any quantum mechanics
proceeding ).

I can edit the “atom property” matrix manually, and put the correct valors
there (when I open "phenolate.out in avogadro), for each atom, but the
program just let me do one by one (for phenolate it’ s okay but for a bigger
system… boring … If possible to “ copy” and “ paste” like in an
spreadsheet would be great too…

So… sorry to bother you…

and thanks a lot.

Em 24 de maio de 2010 11:59, José Fernando Ruggiero Bachega <
ferbachega@gmail.com> escreveu:

Geoffrey Hutchison

I’ḿ generating some ESPs from models minimized by MOPAC2009. The ESP
for Fenol and Fenolate looks strange… or may be wrong… When I active
the option “labels” - with partial charges, Avogadro returns me some partial
charges different from the MOPAC2009 calculated in Gabedit. So Avogadro is
not using the correct charges to produce the ESP… what should I do ?

Can you send me the file? The MOPAC files I’ve seen only have one set of
charges. So I’d be interested to see the actual text.

Geoffrey, Hi, I’ m paris now, and the original files are in brazil, But I’
m gonna try to reproduce the “errors” and send to you as soon as possible.

See Y

And really thanks

Thanks,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

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