You could use coot(or any builder). With coot mutate your SER into a SER which will fill in your heavy atom gaps. Write out the pdb and either use it or copy the atom into your original pdb. Guessing the position would work fine too.<br>
<br><div class="gmail_quote">On 29 May 2010 01:12, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</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 class="im">----- Original Message -----<br>
From: you zou <<a href="mailto:zou.you@live.com">zou.you@live.com</a>><br>
Date: Friday, May 28, 2010 14:41<br>
Subject: [gmx-users] add missing atom<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
</div><div class="im">> Hi everyone,<br>
<br>
<br>
> I have one question about adding atoms that are missing in residue. This atom is OG in SER amino acid. I don't know how can I add this atom to my residue. If I have to add this atom manually how can I find coordinates of that? Or If there is server or software to do this I will be happy if you suggest me its.><br>
<br>
</div>There's no automated GROMACS tool, and I haven't used any other particular tool for the task. For just one atom + hydrogen, you're probably fine to guess approximate coordinates and use EM to fix it.<br>
<font color="#888888"><br>
Mark<br>
</font><div><div></div><div class="h5">--<br>
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