Lester Hedges

H there. Your issue comes at a good time, and is indeed related to `pdb4amber` and the way that `tLEaP` edits the molecule during parameterisation. From the output you can...

This could also be a case of adding a clearer error message that states some possible solutions, e.g. adding the missing atoms yourself, or running `pdb4amber` manually. This might be...

Hi @SofiaBariami, I agree that is kind of a dual Sire/BioimSpace question but I've transferred this issue over here since the issue (for now) is likely specific to the creation...

Much as I'd like to take credit for it, the updated AMBER parser is all @chryswoods work :-)

I'm not completely sure how you are currently constructing a Sire/BioSimSpace system parameterised with the QuBe forcefield, but this is what I think would be the ideal solution... Hopefully you...

Hi @SofiaBariami, I noticed that you recently pushed to the `feature-vSites` branch. Is the `feature_virtual-sites` branch now redundant? If so, I'll delete it since I'd like to avoid a proliferation...

I've now added functionality to _uniquify_ atom names according to the constraints of the PDB format. This removes a series of warnings that I was seeing (which couldn't be supressed)....

Bah, `openforcefield` pulls in `ambertools`, which pulls in `libgcc`, which breaks my Sire development environment so that I can no longer recompile. The environment is in a completely broken state...

Just an update to say that I've merged things across to devel so that users can play around with the current functionality. It looks like there's been an update to...

Thanks for the information, that's useful to know. We normally search for `antechamber` in `${AMBERHOME}/bin` rather than assuming that directory has been added to the path, which isn't always the...