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@umesh-timalsina That should be the case now. I think the `backend` keyword may be helpful for selecting between parmed writer vs mdtraj writer?

Nothing at the moment, I was thinking of implement some rudimentary sorting during the convert RDKit structure step to assert the orders are correct, but I have started nothing yet....

Hi @slenka93, this is because during the saving out of the `box_p`, we do not modify the name of the residue (no appending idx number) which lead to all molecule...

Hi @slenka93, sorry I made a mistake in the comment above, I just checked and there is actually a away to write out all the molecule as independent residue (the...

Hi @slenka93, I was review the code we have (`formats/gsdwriter.py`) and I don't think we explicitly parse residue info at the moment. So that's why everything is lump into one...

unfortunately, I don't think we have that conversion at the moment

you're welcome

Hi @mphoward, it would be great if you can open a PR with the solution posted above!

I will look into the packing functions and see if I can fix it.

Agree with changing the `element` arg to `symbol`, gonna do a quick commit to change the var name