[modeller_usage] ERROR: Radii must all be greater than zero.

[Thomas Evangelidis <>]

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