Xiao-Ping Zhang wrote: > Many proteins are phosphorylated in vivo and and the status of their > phosphorylation correlate to their function. The residues which are > phosphorylated (Thr, Tyr or Ser) can be determined by mass spectrometry. > I wonder how to build a phosphorylated model directly or how to apply a > patch on a model to get a phosphorylated model in Modeller?
Sure - you could build a comparative model in the usual way (assuming you have a template) and phosphorylate the residues you're interested in by applying a suitable patch in the special_patches method. If a suitable patch does not exist, you'll have to add a new one to the topology file - see the FAQ or the CHARMM forums.
If your intention is to take an existing PDB and use Modeller to phosphorylate some residues, Modeller is perhaps not the best package for the job - you'd be better off using a dedicated MD program.
Ben Webb, Modeller Caretaker