[phenixbb] phenix.refine problems with my pdb

[Matthew Bowler]

Thanks for replies so far....

I removed all ligands and then waters - the waters seem to be the  
problem as the protein model is now refining, do they need to be  
treated/marked in a different way for phenix?

Thanks again, Matt.


On 15 Mar 2007, at 13:32, Nicholas Noinaj wrote:

> matt,
>
> 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...
> http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
>
> Again, Best of luck!
>
>
>
> cheers,
> nick
>
>
> -----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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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