Christoph Klein

Should be easy enough to pass that arg through to `force_overlap`. Slightly less pretty question is do you allow users to independently control backfill and guest bonding?

The interface should probably look something along the lines of: `mb.add_surface_ports(surface, binding_site_types='OS')` where `binding_site_types` can be a list of eligible atom names.

Hmmm it might be worth trying out. Any interest in giving it a try? My main worry is that this won't provide the fidelity we really need. We would need...

Just randomly found this. Haven't tried it but looks relevant http://stackoverflow.com/questions/20410501/how-to-estimate-local-tangent-plane-for-3d-points

> sticking them into Forcefield.apply() before the Structure is returned would be a better solution That sounds great 👍

That will be a good starting point. Beyond that the next two priorities will likely be 1. Get things running in OpenMM with `CustomNonbondedForce` 2. Generalize any low hanging fruits...

We've had a couple of folks ask related questions. The responses include a few workarounds and some ideas for how we could implement this without a major change to the...

Ok I'll play around with some color/size combinations and see if I can find one that obviously distinguishes it from other atoms.

The gro parser does not read anything beyond the first letter: https://github.com/mdtraj/mdtraj/blob/master/mdtraj/formats/gro.py#L334 Here's some more context for why this is a harder problem than it sounds like: https://github.com/mdtraj/mdtraj/issues/909