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choderalab / openmoltools

An open set of tools for automating tasks relating to small molecules
MIT License
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Why is generateOEMolFromTopologyResidue line 137 commented out? #279

Closed zhang-ivy closed 4 years ago

zhang-ivy commented 5 years ago

generateOEMolFromTopologyResidue line 137: https://github.com/choderalab/openmoltools/blob/master/openmoltools/forcefield_generators.py#L137

I found that uncommenting 137 and commenting 138 resolves the following error related to incorrect bond perception:

screen shot 2018-09-26 at 9 22 11 am

It seems that using antechamber (instead of bondtype) results in perception of all bonds as single bonds (and therefore misperceiving C-O double bonds). In line 138, I also tried changing -j 2 to -j 4(the default) and am still getting the same error.

I’ve also tested with 1) ambertools installed and ambermini removed (results in the error: ValueError: Cannot find AMBER GAFF) 2) ambermini install and ambermini removed (results in missing parmed package)

Would it be possible to alter generateOEMolFromTopologyResidue so that it uses bondtype to some capacity?