<div dir="ltr">Perhaps using the formal charges according to the residue? That is - Lysine will have an N+, while Aspartate will have two C+0.5?<br>Just a thought...<br clear="all"> <br>Koby Levy research group,<br>Weizmann Institute of Science. <br>
<a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
<br><br><div class="gmail_quote">On Wed, Oct 8, 2008 at 11:36, Berk Hess <span dir="ltr"><<a href="mailto:hessb@mpip-mainz.mpg.de">hessb@mpip-mainz.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="Wj3C7c">Omer Markovitch wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
I just checked the pdb file format.<br>
There is a filed of two characters for the charge of an atom.<br>
But this would only be an integer charge, i.e. the charge of an ion.<br>
Is this what you want, or do you want the partial charges of each<br>
atom?<br>
<br>
Berk<br>
<br>
This is what I intended (charge of an ion).<br>
Or maybe add either option to trjconv?<br>
Thanks! Omer.<br>
</blockquote></div></div>
But things are not that simple.<br>
All atomistic force fields have partial charges on most atoms.<br>
Simple ions such as Na+ or Cl- will have an integer charge.<br>
But something like SO4^-2 or any charged protein residue<br>
has the charge spread out over several atoms.<br>
One can not meaningfully assign an integer charge to a single<br>
atom in such a group.<br><font color="#888888">
<br>
Berk</font><div><div></div><div class="Wj3C7c"><br>
<br>
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