Lester Hedges

Yes, that's a good idea. I believe the gcc pin was for RDKit. It's probably worth asking Exs if we can unpin or update the RDKit version as it's quite...

It actually looks like we only set a minimum version. Perhaps they retained the pin for their internal build so this is hopefully no longer needed.

Just adding [example files](https://github.com/OpenBioSim/sire/files/15161088/posre_bug.tar.gz). The following fails: ```python import sire mols = sr.load("ABFE*") OSError: SireError::io_error: Cannot load the molecules: There is not enough information in this parser (Gro87( title() =...

It does give an informative error if you just read the topology file in isolation, i.e.: ``` This file could not be parsed by any of the file parsers! It...

The sire RMSD alignment just does rigid-body translation and rotations, so I assume that this is failing when the mapping is too large. It seems to work for me if...

Can confirm that I see the same segmentation fault at lambda = 1. Will see if I can trace it.

Just to note that I don't see a mapping from dummy ambertype to dummy ambertype in your example pert files, but this doesn't seem to be the source of the...

For lambda = 1, I can confirm that the segfault occurs on [this](https://github.com/OpenBioSim/sire/blob/843c7f1edec1935d93c9f168d9280eabc6a7f570/wrapper/Tools/OpenMMMD.py#L1641) line of `OpenMMMD.py`. I'll add some debugging statements to the C++ code to see where it's blowing...

Also, the pert files are missing an `endmolecule` record at the end, but again this doesn't seem to affect the segfault. Looking at the output of the parser it seems...

Ah, I see, there is no space in `initial_charge0.00000` for the final record. Printing the line and the words (the records after the line is split) makes it clear what's...