While Mark's answer is entirely complete, I'll just add one more idea
in case you don't know where to put the OG.
1. Go into your .gro file and change the SER to an ALA
2. pdb2gmx to place the hydrogens around the CB
3. EM
4a. Copy the EM output .gro file into 3 directories, and in each one
of them mutate the ALA back to SER, successively replacing a different
HB atom with the OG atom.
4. pdb2gmx to place the hydrogen on the SG
4c. EM
5. Now look at your structures and see if one of them makes any more
sense than the others. If you can't tell, then you can run some MD on
each and ensure that they interconvert. If it's a really essential SER
(like in a binding pocket), you could calculate PMF about chi1.
It all depends on how important it is to get the equilibrium location
of that OG atom -- and it is at least possible that it is very
important (Not only for binding FE calculations, but potentially for
conformation: http://www.ncbi.nlm.nih.gov/pubmed/11053148).
Chris.
-- original message --
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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