Jason Swails

> However, there is another case to be considered - matcher is `None`. Yea, I'd thought about that. I did just now come up with a workaround: ```python _singleton =...

My best guess is that tleap hard codes the assumption that there are either 0 or 2 wild-cards and if the first atom is a wild-card, it assumes the last...

> But if it's Amber that has the error and OpenMM's result is correct, then it's fine regardless of what the magnitude of the difference is. Amber is the reference...

Without providing the PDB file that causes the problem there's really no way to diagnose. If there's a PDB from RCSB that fails to parse, you can just provide the...

It's not ours. It's Michael Word's (he's at OpenEye, I think). We just bundle it because we find it useful: See here: http://kinemage.biochem.duke.edu/software/reduce.php

"Atom Type" is not well-defined in ParmEd because it gets them from all sorts of source file formats. This includes file formats that don't actually have atom types (like OpenMM)...

> Obviously not all of the users are commenting on the github repo in general though, especially if they're only directly use a downstream. Right, but I was wondering if...

For all of Amber we wanted to see where (and how) the windows-compatible bits of Amber out there are being used to help us prioritize what we should do with...

> In the interests of comity and decorum, I will refrain from commenting on the existing Amber build system. haha... it is what it is :). If you ask Amber...

> If I personally worked on Amber, I would strongly advocate changing the build system, Many people have before, even in recent memory. It's not something "outsiders" would have seen,...