I would like to add a GTP residue to a nucleic acid chain. For so I followed the following steps in coot: add monomer from library, GTP, changed chain ID and residue number accordingly, and then Extensions --> Modelling --> link 2 atoms. I got a dashed line between the 3'O of the GTP and the phosphate of the neighboring nucleotide, and then I used the real space refine tool. Up to here, it all looked promising.

In phenix refine I run elbow and readyset and provided cif files, but after phenix.refine I find out that the link between GTP and it's neighbor is gone.

How to preserve the bond?

Thank you very much in advance!! 

Best,

Almudena