Hi!

I was trying to fit my ligands into my model and density. And I have successfully fitted 2 ligands (same molecule) but my 3rd ligand is different molecule.
After fitting my 3rd ligand (with COOT) and merged it with my protein, II created a restraint file with:

  phenix.elbow my_model_coot-0..pdb --do-all --output=all_ligands

It created all_ligand.cif, which I used for in my next refinement with Phenix (GUI). I supplied my density, model and the restraint file and run phenix.refine.
Unfortunatate I'm getting this error message when it starts to run phenix.refine and opening COOT window:

Sorry: Fatal problems interpreting PDB file:

Number of atoms with unknown nonbonded energy type symbols: 1

Please edit the PDB file to resolve the problems and/or supply a

CIF file with matching restraint definitions, along with

apply_cif_modification and apply_cif_link parameter definitions

if necessary (see phenix.refine documentation).

Also note that phenix.elbow is available to create restraint

definitions for unknown ligands.

I have use the same procedure for fitting my first 2 ligands. and it worked. But this time it failed!
What do you think I should do?


Thanks
Hermi