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 <[email protected]> wrote: > ----- Original Message ----- > From: you zou <[email protected]> > Date: Friday, May 28, 2010 14:41 > Subject: [gmx-users] add missing atom > To: [email protected] > > > 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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