I'm trying to obtain refined models of a loop region from a existing pdb
file (a model I built before with modeller). I only want to refine a
loop, and I've followed the steps in
http://www.salilab.org/modeller/manual/node34.html. But it always
appears me this error message:
File "<string>", line 1, in ?
File
"/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py",
line 36, in run
self._runlines(self.lines)
File
"/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py",
line 153, in _runlines
subrout)
File
"/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py",
line 384, in _run_top_cmd
eval('self.topcmds.' + lowcmd + '()')
File "<string>", line 0, in ?
File
"/Library/modeller-9v2/modlib/modeller/top_interpreter/commands.py",
line 230, in optimize
optimization_method=ometh)
File "/Library/modeller-9v2/modlib/modeller/top_interpreter/topcmds.py",
line 412, in optimize
ValueError: read_op_662E> Invalid choice LONG for variable OUTPUT: can
choose one or more from the following: NO_REPORT REPORT
I've tried to change some settings in the .top file but always appear
this error.What can I do?
Another question: if in the model I've built and from which I've to
refine a loop, I had to make a disulfide bridge in this loop, in the
loop refinement I also have to make the disulfide restraint?