[phenixbb] Restraint creation for ligand
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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