[gmx-users] add missing atom

Oliver Grant olymacfoogal at gmail.com
Sat May 29 15:13:38 CEST 2010

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.

On 29 May 2010 01:12, Mark Abraham <mark.abraham at anu.edu.au> wrote:

> ----- Original Message -----
> From: you zou <zou.you at live.com>
> Date: Friday, May 28, 2010 14:41
> Subject: [gmx-users] add missing atom
> To: gmx-users at gromacs.org
> > Hi everyone,
> > 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.>
> 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.
> Mark
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