Lester Hedges

Thanks, both. > ...have bond order and stereochemistry information? I assume no, since it's a PDB file, but I don't know what else is added into this object model. No,...

For reference, how were these files generated in the first place? Also, what water model is used? The AMBER topology parser uses a `discoverMolecules` function to divide the atoms into...

Sire does have a `bondHunter` that can be used to break molecules. However, it's tricky when the molecules already have properties, since these will need to be broken too. Here...

Hi there, For part of question 1): I'm not sure why this happens but I've recently fixed this (last) week by simply re-trying the `trjconv` command if it happens to...

Out of interest, is there are reason why you need to use ParmEd to convert the GROMACS files, rather than using BioSImSpace directly, i.e.: ```python import BioSImSpace as BSS #...

Hi again, I'm really not sure what's going on with those GROMACS files provided in the repository you linked to. Out of interest, I looked at their [example notebook](https://github.com/bayer-science-for-a-better-life/abfe-benchmark/blob/main/burn_in_parameter_generation.ipynb) which...

I've just re-run the above script, instead using ParmEd to write to GROMACS format. As you've found, on conversion to AMBER format within BioSimSpace, any AMBER simulation fails with the...

Out of interest, do the original GROMACS files work with SOMD? (For example, if you just perform minimisation and equilibration with GROMACS rather than PMEMD.) It would be interesting to...

> Could you setup from scratch the input files with BioSimSpace (starting from pdb files extracted from the pmemd equilibration and solvating in BioSimSpace. I tried this myself, but the...

Thanks for this, I should be able to take a look later. The atom number might change because the parsing is done in parallel, so the order might not be...