Adding Custom AtomTypes to Pyrosetta

[Anonymous]

 

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

[Anonymous]

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.

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