[phenixbb] Ligand woes

José Trincão trincao at dq.fct.unl.pt
Tue Jul 5 05:53:00 PDT 2011

Hello all,
I have been having very weird problems refining a structure with several ligands. The weirdest problem is that if I try to run ligand fit giving just the name of the ligands, no problem - it finds the ligands (FAD and MTE). I save the pdb with all the ligands in and phenix.refine complains that MTE is not recognised, I have to run ready-set. I do it. Run phenix.refine again, and now it complains with the following:
 Number of atoms with unknown nonbonded energy type symbols: 116
   "HETATM18439  C1' MTE A3003 .*.     C  "
   "HETATM18441  C2' MTE A3003 .*.     C  "
   "HETATM18443  C3' MTE A3003 .*.     C  "
   "HETATM18444  O3' MTE A3003 .*.     O  "
   "HETATM18474  N9A FAD A3005 .*.     N  "
   "HETATM18475  C8A FAD A3005 .*.     C  "
   "HETATM18476  N7A FAD A3005 .*.     N  "
   "HETATM18477  C5A FAD A3005 .*.     C  "
   "HETATM18478  C6A FAD A3005 .*.     C  "
   "HETATM18480  N1A FAD A3005 .*.     N  "
   ... (remaining 106 not shown)

Any help will be greatly appreciated.


José Trincão, PhD	CQFB at FCT-UNL
2829-516 Caparica, Portugal

"It's very hard to make predictions... especially about the future" - Niels Bohr

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