| Detailed description |
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Here is an example of an exception that may be thrown during the reading of CHARMM topology files, particularly with Python 3:
Traceback (most recent call last):
File "/home/khaos/prog/openmm-6.3/lib/python3.4/site-packages/simtk/openmm/app/charmmparameterset.py", line 522, in readTopologyFile
elem = words[4]
IndexError: list index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "openmm_run.py", line 33, in <module>
params = read_params(inputs.toppar_path)
File "/panfs/pfs.acf.ku.edu/research/khaos/Test/OpenMM_Error/OpenMM_Python3.4_Error/omm_readparams.py", line 33, in read_params
params = CharmmParameterSet( *parFiles )
File "/home/khaos/prog/openmm-6.3/lib/python3.4/site-packages/simtk/openmm/app/charmmparameterset.py", line 137, in __init__
for top in tops: self.readTopologyFile(top)
File "/home/khaos/prog/openmm-6.3/lib/python3.4/site-packages/simtk/openmm/app/charmmparameterset.py", line 526, in readTopologyFile
masselem = Element.getByMass(mass)
File "/home/khaos/prog/openmm-6.3/lib/python3.4/site-packages/simtk/openmm/app/element.py", line 126, in getByMass
Element._elements_by_mass[elem.mass] = elem
File "/tools/cluster/6.2/python/3.4.2/lib/python3.4/collections/__init__.py", line 63, in __setitem__
if key not in self:
TypeError: unhashable type: 'Quantity'
This is fixed in master, though. |
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