[phenixbb] Restraint creation for ligand

Hermella Woldemdihin hermifi at yahoo.com
Tue Aug 10 06:58:41 PDT 2010


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 
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 
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?


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