[phenixbb] phenix.refine problems with my pdb

Nicholas Noinaj noinaj at uky.edu
Thu Mar 15 06:32:30 PDT 2007


can't offer much help, but have you tried to remove the ligand and try refinement?  it would let you know if the pdb file or the presence of the ligand is the problem.  at least let you would know where you should focus your attention.  

if all else fails, have you tried getting parameters for your ligand from the PRODRG Server and using that for inputing the ligand parameters into phenix.refine directly when you setup the refinement job?  (I think i have done this before???)

here is the website in case you aren't familiar...

Again, Best of luck!


-----Original Message-----
From: Matthew Bowler <mwb at mrc-dunn.cam.ac.uk>
To: phenixbb at phenix-online.org
Date: Thu, 15 Mar 2007 13:00:42 +0000
Subject: [phenixbb] phenix.refine problems with my pdb

Dear All,
	I am trying to run phenix.refine but I keep getting the message:

Sorry: Fatal problems interpreting PDB file:
   Number of atoms with unknown nonbonded energy type symbols: 308
   Please edit the PDB file to resolve the problems and/or supply a
   CIF file with matching restraint definitions. Note that
   elbow.builder is available to create restraint definitions.

I have run my ligands through elbow and used the output .cif but I  
still get the same message.  I can find no info on this problem in  
the manual or the BB, can anyone help?  Thanks in advance, yours, Matt.

Matthew Bowler
MRC Dunn Human Nutrition Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge CB2 2XY
Tel: 0044 (0) 1223 252826
Fax: 0044 (0) 1223 252825

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