Xia,Wei wrote: > It seems that the hydrogen names in Modeller results are HB1, HB2 > However IUPAC and many other software would use 'HB2 HB3' names. > Is there any options in Modeller that I can choose or any scripts to use to > convert the format?

Modeller generates output PDB files that are consistent with post-remediation PDB structures. If you still have software that expects pre-remediation PDB format, the easiest solution is probably to write a short script to convert the atom names in the output PDB files.

Ben Webb, Modeller Caretaker