Mary Pitman

Just following up, could you share the script that you guys used to produce an XML file that had the correct bond terms for a complex with both protein and...

Thanks for the pointers @diogomart @kntkb > Thank you for your help. We redid the XML file generation for espaloma and amber and now they have the same bond count....

This is more for users, but if anybody is running into this issue, one option is to downgrade pymbar, but if you want to continue with pymbar version 4.0 you...

@acadiaconnor if you end up having other issues (I'm not using many of the functions from pyemma) you might double check which numpy loads into your Jupyter notebook.