Lester Hedges

I had previously looked at the specification at the end of [this](http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf) document, although it is quite technical to implement this in code. Someone is currently working on a Mol2...

Thanks for this. I had also noticed this the other day when I checked their recipe having discovered that version 4 pulls in `cudnn` and `jaxlib`, which come to over...

Hi there, I'll be able to take a better look at this tomorrow. Just to check, here are the `forcefled` properties for the two molecules: ```python import BioSimSpace as BSS...

Yes, I see the issue. As I mentioned, the scale factors are being set incorrectly when going to AMBER format. (Not yet sure if it's on read or write.) Here's...

If I analyse the `AmberNB14` terms from the `parameters` object of the second system (the initial AMBER conversion) I see that the values are correct, even though those listed in...

The following code in [amberprm.cpp](https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireIO/amberprm.cpp#L1094) sets the `forcefield` property on read. Essentially, unless the property already exists in the user map, it generates a _default_ based on assumptions about the...

Thanks, @chryswoods, that makes sense. I had written code to do what you suggested regarding scanning the `AmberNB14` values after they had been created, then using that the determine the...

@jmichel80 Yes, that could be a good option.

Thanks, those are good suggestions. I totally agree about not liking warning messages, which is why I have pretty much suppressed everything from third-party libraries, or caught the warning and...

The `map` keyword is already fully exposed throughout BioSimSpace so we can use that if needed. I agree with @chryswoods that information would ideally be in the topology file, since...