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openmm / pdbfixer

PDBFixer fixes problems in PDB files
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Trying to create SystemGenerator from RDKit converted openff topology #200

Closed tarungog closed 4 years ago

tarungog commented 4 years ago

Hello,

image

Can someone explain this error to me? It happens at the create_system line. AttributeError: 'Topology' object has no attribute 'getPeriodicBoxVectors'

peastman commented 4 years ago

It looks like this is a question about openforcefield, not PDBFixer. I don't see any PDBFixer classes in there.

jchodera commented 4 years ago

@tarungog : In future, could you open issues in https://github.com/openmm/openmmforcefields?

It looks like the issue is that you're feeding an openforcefield.topology.Topology object to ofmol.to_topology(), but it instead expects a simtk.openmm.app.Topology.

Try changing ofmol.to_topology() to ofmol.to_topology().to_openmm().

tarungog commented 4 years ago

ahh sorry! got the wrong repo. closing it out, thanks for the pointer @jchodera.

Edit: would you mind looking at this ticket here? https://github.com/openmm/openmmforcefields/issues/103