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?
On 4/21/10 10:20 AM, Thomas Evangelidis wrote: > 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:
In order to calculate the GB/SA interaction between the loop and the ligand, Modeller needs to know the radii of all atoms in the ligand. You'll need to modify solv.lib as suggested to add radii for each atom type in ATP. I can't tell you what values to use, since they have not been parameterized, but you could simply copy those for similar-looking atom types. Alternatively, use the regular loopmodel class, which does not include GB/SA.
There will be an automatic workaround for this issue in the upcoming 9v8 release; ligand atoms will simply be treated as having a very small (but non-zero) radius for GB/SA.
Ben Webb, Modeller Caretaker