[phenixbb] phenix.refine problems with my pdb

[Nicholas Noinaj]

matt, 

>>> Number of atoms with unknown nonbonded energy type symbols: 308

just curious, did you have 308 waters?  as peter said, hard to determine exact problem without some files or examples to look at.  also phenix does a good job with water picking, in my little experience.

just one more question, when you do get the refinement to work, is your ligand(s) included with the protein model?  just no waters, right?  it wasn't completely clear from your message.  if the ligands aren't included, i recommend adding it(them) back and see if refinement works.  then if that works, try water picking within phenix.


again, best of luck.



cheers, 
nick


-----Original Message-----
From: Matthew Bowler <mwb at mrc-dunn.cam.ac.uk>
To: noinaj at uky.edu, PHENIX user mailing list <phenixbb at phenix-online.org>
Date: Thu, 15 Mar 2007 14:15:45 +0000
Subject: Re: [phenixbb] phenix.refine problems with my pdb

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