[phenixbb] Restraint creation for ligand

Tom Terwilliger terwilliger at lanl.gov
Tue Aug 10 07:12:55 PDT 2010

Hi Hermi,
Is it possible that the names of your ligands are the same (e.g.,  
"LIG")? If that is the case, you may be able to solve the problem just  
by renaming one of them. If that isn't it, I'll be happy to have a  
look if you want to send the 2 ligand PDB files.
All the best,
Tom T

On Aug 10, 2010, at 7:58 AM, Hermella Woldemdihin wrote:

> 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
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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