Dear All,
Recently I generated a dataset of DNA protein complex.
I built the DNA model with the simple mutate of nucleic acids, however when I
tried to refine my structure, I came to the fatal error below with unknown
bonded energy atom.
(Similar to the phenix Tutorial 10: Generating ligand coordinates and
restraints for structure refinement):
Number of atoms with unknown nonbonded energy type symbols: 16
" N ABN A 246 "
" C ABN A 246 "
" C1 ABN A 246 "
" C2 ABN A 246 "
" C3 ABN A 246 "
" C4 ABN A 246 "
" C5 ABN A 246 "
" C6 ABN A 246 "
" N ABN A 247 "
" C ABN A 247 "
Further, Phenix.ready and Phenix.eLBOW were used to generated the restraints
information, however nothing extra restraints information was got phenix.eLBOW.
I assumed that the phenix.eLBOW recognized the nucleic acids from the coot
“simple mutate” as compatible with Phenix but still I can’t use phenix.refine
to refine this model.
So how can I force the phenix.eLBOW to generate the restraints? or is there any
other software could be used to generate the cif file?
Many thanks,
Yurong
