Hello everyone,
Does anyone have experience adding custom atom types to Pyrosetta? I have tried creating my own `atom_properties.txt` file, shown below.
```
NAME ATOM LJ_RADIUS LJ_WDEPTH LK_DGFREE LK_LAMBDA LK_VOLUME
A1 X 2.0000 0.0486 1.0000 3.5000 23.7000
A2 X 2.0000 0.2000 1.0000 5.0000 23.7000
VIRT VIRT 0.0000 0.0000 0.0000 3.5000 0.0000 VIRTUAL
```
However, when I try to add these atoms to the chemical database, using `pyrosetta.rosetta.core.chemical.AtomTypeSet(‘path/to/atom/type/set’)` and `pyrosetta.rosetta.core.chemical.add_atom_type_set_parameters_from_command_line(‘full_atom’, custom_atom_typeset)`, PyRosetta fails to recognize any residues with these atom names in them. Is there any more documentation on adding new AtomTypes to PyRosetta?
Thanks,
Lenny
Rosetta (and PyRosetta) really isn't set up for adding new AtomTypes "on the fly". Your best bet is to make a copy of the Rosetta database, put your new atom types in the appropriate location in the files there, and point your PyRosetta instance to that database during initialization.