I've been attempting to use prefmd2 to refine some models I've generated. I think I've installed everything correctly. When I run it, it run for a couple minutes, and then it errors out.
This is the output I've received
Starting the 'init' stage.
- Preparing the working directory...
- Removing hydrogens from the initial model...
- Completed the 'init' stage.
Starting the 'locprefmd' stage.
- Running locPREFMD for local refinement on init.pdb ...
- Completed the 'locprefmd' stage.
Starting the 'topology' stage.
- Defining topology...
- Completed the 'topology' stage.
Starting the 'equilibration' stage.
- A total of 1 equilibration tasks will be run.
- Running equilibration task 1...
Traceback (most recent call last):
File "prefmd2.py", line 310, in
equil.run(job=job)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/equil.py", line 84, in run
run_tasks(job, task_s)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/equil.py", line 155, in run_tasks
libcommon.asystem(module="exec_equil", args=cmd)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/libcommon.py", line 132, in asystem
raise e # The finally block is run before this.
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/libcommon.py", line 130, in asystem
getattr(import_module(module), func)(args)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/exec_equil.py", line 222, in main
run(input_pdb, arg.output_prefix, options, arg.verbose, arg.non_standard)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/exec_equil.py", line 164, in run
pdb = mdtraj.load(init_pdb.short())
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/core/trajectory.py", line 433, in load
value = loader(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/pdb/pdbfile.py", line 153, in load_pdb
with PDBTrajectoryFile(filename, standard_names=standard_names) as f:
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/pdb/pdbfile.py", line 269, in init
self._read_models()
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/pdb/pdbfile.py", line 561, in _read_models
self._topology.create_disulfide_bonds(self.positions[0])
IndexError: index 0 is out of bounds for axis 0 with size 0
I've been attempting to use prefmd2 to refine some models I've generated. I think I've installed everything correctly. When I run it, it run for a couple minutes, and then it errors out.
This is the output I've received
Starting the 'init' stage.
Starting the 'locprefmd' stage.
Starting the 'topology' stage.
Starting the 'equilibration' stage.
Traceback (most recent call last):
File "prefmd2.py", line 310, in
equil.run(job=job)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/equil.py", line 84, in run
run_tasks(job, task_s)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/equil.py", line 155, in run_tasks
libcommon.asystem(module="exec_equil", args=cmd)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/libcommon.py", line 132, in asystem
raise e # The finally block is run before this.
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/libcommon.py", line 130, in asystem
getattr(import_module(module), func)(args)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/exec_equil.py", line 222, in main
run(input_pdb, arg.output_prefix, options, arg.verbose, arg.non_standard)
File "/uufs/chpc.utah.edu/common/home/u1261874/prefmd2/prefmd2/scripts/exec_equil.py", line 164, in run
pdb = mdtraj.load(init_pdb.short())
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/core/trajectory.py", line 433, in load
value = loader(filename, **kwargs)
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/pdb/pdbfile.py", line 153, in load_pdb
with PDBTrajectoryFile(filename, standard_names=standard_names) as f:
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/pdb/pdbfile.py", line 269, in init
self._read_models()
File "/uufs/chpc.utah.edu/common/home/u1261874/software/pkg/miniconda3/lib/python3.7/site-packages/mdtraj/formats/pdb/pdbfile.py", line 561, in _read_models
self._topology.create_disulfide_bonds(self.positions[0])
IndexError: index 0 is out of bounds for axis 0 with size 0