key "HB1" not found in forcefield about molly.jl

[jgreener64]

This certainly is an area where Molly is lacking features at the moment. In this case it looks like the atom names in the PDB file are different from those in the XML force field. Currently they have to match exactly, whereas more mature software matches residues based on topology and allows different atom names.

This issue can be left open to track this. In the mean time I would consider using OpenMM's protein preparation tools, which should match their force field file better. The system you get out won't be directly comparable to the Gromacs system, but depending on system size you may struggle to sample long enough with Molly to make a direct comparison anyway.

All of this will hopefully be fixed long term. More robust setup tools is on the todo list but not at the top.