[phenixbb] Restraint creation for ligand

sbiswas2 at ncsu.edu sbiswas2 at ncsu.edu
Tue Aug 10 08:18:19 PDT 2010

If the ligands are joined covalently then a single cif file will work in
coot. However if they are separated, you might want to make a different
cif file rather than combining the three.

> 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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