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.