[phenixbb] BRU error

[Krystle Williams McLaughlin]

Hi,
I'm using phenix for refinement and I keep getting an error. 
My DNA strand has a bromo-uridine in it and phenix.refine keeps crashing on this nucleotide. 
Here is the error:

Number of atoms with unknown nonbonded energy type symbols: 40
    "ATOM   2770  P   BRU P   5 .*.     P  "
    "ATOM   2771  O1P BRU P   5 .*.     O  "
    "ATOM   2772  O2P BRU P   5 .*.     O  "
    "ATOM   2773  O5* BRU P   5 .*.     O  "
    "ATOM   2774  C5* BRU P   5 .*.     C  "
    "ATOM   2775  C4* BRU P   5 .*.     C  "
    "ATOM   2776  O4* BRU P   5 .*.     O  "
    "ATOM   2777  C1* BRU P   5 .*.     C  "
    "ATOM   2778  N1  BRU P   5 .*.     N  "
    "ATOM   2779  C6  BRU P   5 .*.     C  "
    ... (remaining 30 not shown)

Here is what I have in my pdb: 

ATOM   2901  P   BRU E   5      33.977 -16.324  24.303  1.00 27.21           P
ATOM   2902  O1P BRU E   5      34.027 -15.724  22.919  1.00 28.22           O
ATOM   2903  O2P BRU E   5      33.857 -15.340  25.393  1.00 25.06           O
ATOM   2904  O5* BRU E   5      32.721 -17.236  24.418  1.00 28.02           O
ATOM   2905  C5* BRU E   5      32.487 -18.228  23.495  1.00 28.50           C
ATOM   2906  C4* BRU E   5      31.047 -18.347  23.082  1.00 32.59           C
ATOM   2907  O4* BRU E   5      30.337 -18.858  24.152  1.00 28.61           O
ATOM   2908  C1* BRU E   5      29.369 -17.891  24.535  1.00 29.63           C
ATOM   2909  N1  BRU E   5      29.279 -17.855  25.962  1.00 29.72           N
ATOM   2910  C6  BRU E   5      30.426 -17.755  26.799  1.00 30.57           C
ATOM   2911  C5  BRU E   5      30.251 -17.738  28.232  1.00 30.89           C
ATOM   2912 BR   BRU E   5      31.869 -17.591  29.321  1.00 57.08          Br
ATOM   2913  C4  BRU E   5      28.917 -17.845  28.826  1.00 30.70           C
ATOM   2914  O4  BRU E   5      28.768 -17.825  30.033  1.00 29.36           O
ATOM   2915  N3  BRU E   5      27.785 -17.945  27.981  1.00 29.36           N
ATOM   2916  C2  BRU E   5      27.961 -17.966  26.552  1.00 29.05           C
ATOM   2917  O2  BRU E   5      26.994 -18.064  25.848  1.00 35.29           O
ATOM   2918  C3* BRU E   5      30.464 -17.006  22.751  1.00 34.58           C
ATOM   2919  C2* BRU E   5      29.845 -16.605  23.968  1.00 33.10           C
ATOM   2920  O3* BRU E   5      29.526 -17.213  21.768  1.00 37.93           O

I have already run a BRU molecule through ReadySet and when I use the cif file generated from this phenix.refine will run through but when the Bromine atom is in the structure has a large negative density peak in the Fo-Fc map. 
I think it may just be a naming thing. BRU is already in the monomer library so I don't understand why I get an error at first also without the readyset cif file. 
Any suggestions? 

Thanks,
Krystle

 		 	   		  
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