Lester Hedges

Okay, I've figured it out. The issue is because the calcium ion has the same chain identifier, despite coming _after_ the TER record in the PDB. When the PDB is...

I've made a few tweaks to preserve HETATM records and make sure that the TER entry has the correct number. (This doesn't solve this issue, but was an error that...

Thanks for the comments. With regards to the TER / HETATM, I've looked at some of our example files and a few from the PDB and annoyingly the formatting is...

I've looked more at how `HETATM` appear in files from the PDB and there seems to be no standard, so I don't think our modified approach is valid, since it...

For example, in [this](https://www.rcsb.org/structure/7UZO) there a `HETAM`s with the same chain identifier before _and_ after the `TER`. Some examples of the different formatting: `HETATM` in chain `B` before _and_ after...

For what it's worth, changing the chain identifier of the `HETATM` from A to B, i.e. ``` ATOM 1730 HD22 ASN A 120 27.964 7.481 -4.330 1.00 40.77 H TER...

Hi @cespos, I have been working on some improvements to our PDB parser, particularly in terms of the handling of `HETATM` and `TER` records. I am currently testing my edits...

I see no reference to `[ intermolecular_interactions ]` in the Sire [GroTop](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireIO/grotop.cpp) parser, so assume that this is unsupported for now. I imagine that optional sections could be patched in...

Yes, something like this should be possible. Are similar interactions needed for a general ABFE implementation, e.g. would you need to do a similar thing if working with another engine,...

This is already the case with the existing API. System properties aren't associated with molecules and are only preserved when manipulating an existing system, e.g. adding a molecule. If you...