I could be completely wrong here, but I would expect partial charges
to indeed mean charges that can be non-integer but not necessarily
limited between -1.0 and 1.0. These i would consider fractional charges.
For instance I could consider a computational program to calculate a
partial charge of ion in solution (or in a molecule) to be +2.45 as
opposed to a formal charge of +4. In that respect I would expect them
to be more like the Mulliken charges some programs calculate (or
other schemes they have to assign a charge to an atom).
René
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
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] ...
(perhaps to
be expanded a wee bit)
- Partial charges are floats in the range [-1.0, +1.0]
- ionic == formal
I have no idea how closely this correlates with more realistic
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
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
files. The
mmCIF spec is a little more formal. That will tell you how the
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
difference
[smile].
Thank you for your leniency :-)
Miguel
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