Thank You Lennart!

I have replaced with the atom name of N. Now the script works. But because I replaced only one atom, the OH2, just for this N atom has coordinates, the O and OM have not, of course. I would like to assign coordinates for O and OM too. If I replace the one of the H atoms of the water molecules by O, there are also no coordinates for OM. Anyway how can a I do this? How can I define a second atom selection?

I have also tried to write out pdb file from this running and regenerate the structure from a pdb which contains just the N atoms. In that case, CHARMM added 9999.0009999.0009999.000 coordinates for the O and OM.

Do You have any suggestion have can I solve this problem?

Thank You in advance,
Aniko