[gmx-developers] adding formal charges in trjconv

[ggroenh]

If it is for visualization purposes (which is what I assume), can't  
you use the B-factor field?

Gerrit
On 8 Oct 2008, at 11:59, Berk Hess wrote:

> 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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--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/ggroenh/index.html