zzj wrote: > Hi, the problem was solved by deleting "inifile = 'mgl.pdb'" in my > script. mgl.pdb is my template pdb file, without any further change. If > you still think this is not normal, I'll send the input files towrrow > when I get to lab.

If you specify an "inifile" it needs to be a set of coordinates of your model (usually from a previous optimization), not a template. If you leave out "inifile", then Modeller will automatically build an initial model (with a .ini file extension) based on your template(s) and the alignment. This is usually what you want, although sometimes the .ini file has such a bad structure (e.g. knots in the sequence or other bad clashes) that the optimization is unable to recover, and you may be able to manually tweak the initial model to correct this.

Unfortunately, Modeller does very little checking on a user-provided initial model, and expects it to match the .ini file (i.e. same residue and atom order, just with different coordinates). So you can get weird errors if this is not the case.

Ben Webb, Modeller Caretaker