[gmx-developers] adding formal charges in trjconv

Berk Hess hessb at mpip-mainz.mpg.de
Wed Oct 8 11:36:31 CEST 2008

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.


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