Closed leeping closed 10 years ago
I fixed the error with 25a98ae. Your example now gives the error
>>> system = forcefield.createSystem(topology,nonbondedMethod=PME,constraints=HBonds
... ,rigidWater=True,nonbondedCutoff=1.0*nanometer,useDispersionCorrection=True,vdwC
... utoff=1.0*nanometer,polarization=mutual,polar_eps=1e-05,ewaldErrorTolerance=0.00
... 05)
Traceback (most recent call last):
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/bin/openmm", line 7, in <module>
execfile(__file__)
File "/home/rmcgibbo/projects/openmm-cmd/openmm", line 1069, in <module>
openmm.start()
File "/home/rmcgibbo/projects/openmm-cmd/openmm", line 844, in start
system = forcefield.createSystem(topology, **system_options)
File "/home/rmcgibbo/.pythonbrew/venvs/Python-2.7.3/sci/lib/python2.7/site-packages/simtk/openmm/app/forcefield.py", line 328, in createSystem
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
ValueError: No template found for residue 1 (HOH). The set of atoms is similar to HOH, but it is missing 1 extra particles. You can add them with Modeller.addExtraParticles().
Perfect, that is the error I wanted it to have. :)
Okay. Closing this then.
Oops. Sorry.
Hi Robert,
Running the OpenMM command line app with the config file produced the following error. I attached the inputs. Over the next few days, it seems we might want to iron out the config file parsing before posting the public beta.
https://dl.dropboxusercontent.com/u/5381783/input.tar.gz