AttributeError: module 'simtk.openmm.app.forcefield' has no attribute '_matchResidue'

[tengjieksee]

Hi, I was trying to run the setup-protein.sh with my own protein in the example folder "t4-lysozyme". Here's the error,

Preparing receptor by adding missing atoms... Traceback (most recent call last): File "/vcp1/ustudent/tsee0001/.conda/envs/yanky_v3/bin/pdbfixer", line 6, in sys.exit(pdbfixer.pdbfixer.main()) File "/vcp1/ustudent/tsee0001/.conda/envs/yanky_v3/lib/python3.6/site-packages/pdbfixer/pdbfixer.py", line 1238, in main fixer.addMissingAtoms() File "/vcp1/ustudent/tsee0001/.conda/envs/yanky_v3/lib/python3.6/site-packages/pdbfixer/pdbfixer.py", line 903, in addMissingAtoms forcefield = self._createForceField(newTopology, False) File "/vcp1/ustudent/tsee0001/.conda/envs/yanky_v3/lib/python3.6/site-packages/pdbfixer/pdbfixer.py", line 1125, in _createForceField if any(app.forcefield._matchResidue(residue, t, bondedToAtom) is not None for t in forcefield._templateSignatures[signature]): File "/vcp1/ustudent/tsee0001/.conda/envs/yanky_v3/lib/python3.6/site-packages/pdbfixer/pdbfixer.py", line 1125, in if any(app.forcefield._matchResidue(residue, t, bondedToAtom) is not None for t in forcefield._templateSignatures[signature]): AttributeError: module 'simtk.openmm.app.forcefield' has no attribute '_matchResidue'

Any help would be greatly appreciated! :(

[andrrizzi]

Hi @tengjieksee . I think I saw that error before. It seems to be pdbfixer from the stack. Maybe that script is missing the call to fixer.findMissingAtoms() before fixer.addMissingAtoms()? I think taking a look at the pdbfixer manual should help anyway: http://htmlpreview.github.io/?https://raw.github.com/pandegroup/pdbfixer/master/Manual.html .