[gmx-developers] adding formal charges in trjconv

[Berk Hess]

There are only two characters available for the charge on the ATOM line.
We can therefore only have integer charges, e.g. -1, -2, etc.
I think the only option would be to write charges only for atoms with 
integer charge
and zero otherwise.

Berk

Omer Markovitch wrote:
> Perhaps using the formal charges according to the residue? That is - 
> Lysine will have an N+, while Aspartate will have two C+0.5?
> Just a thought...
>  
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
>
>
> On Wed, Oct 8, 2008 at 11:36, Berk Hess <hessb at mpip-mainz.mpg.de 
> <mailto:hessb at mpip-mainz.mpg.de>> wrote:
>
>     Omer Markovitch wrote:
>
>
>
>            I just checked the pdb file format.
>            There is a filed of two characters for the charge of an atom.
>            But this would only be an integer charge, i.e. the charge
>         of an ion.
>            Is this what you want, or do you want the partial charges
>         of each
>            atom?
>
>            Berk
>
>          This is what I intended (charge of an ion).
>         Or maybe add either option to trjconv?
>         Thanks! Omer.
>
>     But things are not that simple.
>     All atomistic force fields have partial charges on most atoms.
>     Simple ions such as Na+ or Cl- will have an integer charge.
>     But something like SO4^-2 or any charged protein residue
>     has the charge spread out over several atoms.
>     One can not meaningfully assign an integer charge to a single
>     atom in such a group.
>
>     Berk
>
>
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