Jonathan Winger wrote: > I'm using Modeller 9v2. My protein is a homodimer, and my template is > also a homodimer. There is one molecule of AMPCPP and 2 metals bound to > each chain of the template. I adjusted the PDB file (2BW7) so that the > metals and nucleotides followed directly after the appropriate chain > TER's. I should add that the modeling runs fine in the absence of > nucleotide.
You could try using the BLK residue type (.) instead of GTP (y) in your model sequence - it is entirely possible that the CHARMM forcefield parameters for GTP are not doing a great job. As for your metal, your model contains MG but your template contains CA, so since you have no equivalent template atom, the MG gets no homology-derived restraints on it and it can wander (Modeller is not smart enough to recognize automatically that one metal could be considered equivalent to another here.) To fix that, you could either create manual distance restraints on your metal ion to hold it in place, or edit your template PDB and change the metal ion there to MG.
Ben Webb, Modeller Caretaker