[gmx-developers] adding formal charges in trjconv

Omer Markovitch omermar at gmail.com
Wed Oct 8 11:44:44 CEST 2008

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.

On Wed, Oct 8, 2008 at 11:36, Berk Hess <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
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20081008/184bc36c/attachment.html>

More information about the gromacs.org_gmx-developers mailing list