How to add an atom to a residue of a given universe, ore replace a residue

[Paolus]

Hi all,

I am wondering if it is possible to add an atom to a residue. The situation is the following: 

- I am reading a simulation trajectory involving deprotonated residues

- For a given time of the trajectory, I want to write a PDB file, but with an added hydrogen 

   for a certain number of deprotonated residues. 

I know how to save a .pdb file for the given trajectory at a given time, no problem with that. But I want to modify the universe of the trajectory to replace one given deprotonated residue with a protonated one. This implies adding an atom and eventually a few topological elements to this universe. I found that it is possible to add topologies, such as bonds, dihedrals, bending etc, but I can't add an atom or replace a given residue?

Is this even possible?

Thanks

Paulus

[Micaela Matta]

Hi Paulus,

yes, it's possible to modify atoms in a Universe. Have a look at the examples here:

 https://userguide.mdanalysis.org/stable/examples/constructing_universe.html#Adding-a-new-segment 
All the best,

Micaela