[phenixbb] Ligand woes
trincao at dq.fct.unl.pt
Tue Jul 5 05:53:00 PDT 2011
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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