Dear Modellers,
I want to build models of a protein with ATP with the dopehr_loopmodel method. The problem is when I include ATP in the alignmnet I get the following error:
Traceback (most recent call last): File "./build_model_parallel.py", line 28, in <module> results = j.run_all_tasks() File "/usr/lib64/python2.6/site-packages/modeller/parallel/job.py", line 127, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib64/python2.6/site-packages/modeller/parallel/job.py", line 160, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib64/python2.6/site-packages/modeller/parallel/job.py", line 176, in _process_event task = obj.task_results() File "/usr/lib64/python2.6/site-packages/modeller/parallel/slave.py", line 61, in task_results r = self.get_data(allow_heartbeat=True) File "/usr/lib64/python2.6/site-packages/modeller/parallel/communicator.py", line 84, in get_data (cmdtype, obj) = self._recv() File "/usr/lib64/python2.6/site-packages/modeller/parallel/communicator.py", line 125, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: <class '_modeller.ModellerError'>: e_gbsa__234E> Atom 1795 (type 94) has GB/SA radius 0.0000. Radii must all be greater than zero. Please edit the library file (e.g. modlib/solv.lib) to set a correct radius for this atom type.
I'm not sure what radii I have to set and to what values. Is there any workaround with this?
thanks, Tom