Hello!
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
outs = _modeller.mod_top_optimize(mdl, edat, libs, *args)
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?
Thank you!! Laura