[ghemical-devel] Specifying state of atom

Tommi Hassinen thassine at messi.uku.fi
Tue Feb 20 09:01:54 EST 2007


Hmm.... I'm not sure if I understood right the original question ; did you 
mean how to set the formal charge in the user interface or in the code?

In the user interface you have to do this :

1) open or draw your molecule
2) select from popup menu : Render / Label Mode / Index
this will show you the atom numbers (or indices) used by the program
internally. See the index of the atom you wish to set the charge.
3) select from popup menu : Enter a Command ; a Command Interpreter box 
will appear. For example if you wish to set formal charge -1 to the atom 
with index 5 you should type in a command:

 	set_formal_charge 5 -1

That's it. Then you can select from popup menu Render / Label Mode / 
Formal Charge to check that everything is the way you wanted.

I can't tell you a code example right now, but perhaps you should look at 
the code in GAMESS interface.

Regards,

 	Tommi


On Tue, 20 Feb 2007, Per Jr. Greisen wrote:

> Hi Tommi,
>
> Thanks for the answer - I am a little puzzled on how the syntax should be
> exactly. If I for an example have lithium and a water molecule how would one
> directly specify that it has a charge of +1 f.ex.
>
> $BASIS GBASIS=STO NGAUSS=3 $END
> $CONTRL SCFTYP=UHF RUNTYP=OPTIMIZE $END
> $SYSTEM TIMLIM=600 MWORDS=6.25 $END
> $DATA
> untitled
> C1
> Li        3,0       -2,416862       -0,337141        0,000000
> O        8,0        0,484172        0,286425        0,000000
> H        1,0        1,335709        0,707575        0,000000
> H        1,0        0,596980       -0,656858        0,000000
> $END
>
> Thanks in advance.



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