Ben, I don't think this is the problem. The atom index I used for the restraint instructions corresponds already to the ini file generated, not the template.
Cardenas, Alfredo wrote:
I have a problem creating a model for a small protein with two zinc atoms. I use the ADD_RESTRAINT commands to create distance restrictions between the zincs and the residues attached to them. Looking at the log file, it looks that the restrictions are read without problems but at the end some ini file is read and I get an Atom index is out of bounds message. I am attaching the top, alignment and log file. I would appreciate any help.
You should check your initial model file (the .ini file) to make sure that the atom numbers you've given in your restraints match the model.
They must match the model, not the template.
Ben Webb, Modeller Caretaker