Re: [Jmol-developers] Formal charges in pdb files

[<rka...@ri...>]

I could be completely wrong here, but I would expect partial charges =20
to indeed mean charges that can be non-integer but not necessarily =20
limited between -1.0 and 1.0. These i would consider fractional charges.

For instance I could consider a computational program to calculate a =20
partial charge of ion in solution (or in a molecule) to be +2.45 as =20
opposed to a formal charge of +4. In that respect I would expect them =20=

to be more like the Mulliken charges some programs calculate (or =20
other schemes they have to assign a charge to an atom).

Ren=E9

On Dec 7, 2005, at 6:20 PM, Miguel wrote:

>>> The issue is how to handle formal charges.
>>>
>>> In the case of .pdb files the charge data is stored in columns 79 &
>>> 80.
>>>> As to charges, I suppose 'charge' could be considered to be 'formal
>>>> charge'
>>>
>>> That is what I thought it was.
>>
>> Why do you think so?
>
> Because within my (naive) binary-world-view there are only two =20
> types of
> charges ... formal and partial ... :-)
>
> Here is the model that is in my head and that is implemented in Jmol:
>
>  - Formal charges are integer values in the range [-4, +7] ... =20
> (perhaps to
> be expanded a wee bit)
>
>  - Partial charges are floats in the range [-1.0, +1.0]
>
>  - ionic =3D=3D formal
>
> I have no idea how closely this correlates with more realistic =20
> models of
> reality. :-)
>
>> The PDB guide (quoted in my previous post) says
>> 'charge', not formal charge. And the examples in the PDB guide are
>> certainly consistant with ionic charge.
>
> Well, they cannot be partial charges because there is no space for =20
> them.
>
>> Of course there may be more description somewhere
>> else in the PDB specs, but I'd like to see it.
>
> I doubt it.
>
> I would look and see how they convert these charges into mmCIF =20
> files. The
> mmCIF spec is a little more formal. That will tell you how the =20
> people at
> the PDB interpret this field.
>
>>> I have no idea what the difference is between these terms.
>>
>> For the moment, Miguel, I'm not going to ask you to learn the =20
>> difference
>> [smile].
>
> Thank you for your leniency :-)
>
>
> Miguel
>
>
>
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