FAQ: Frequently Asked Questions
Table of Contents
1.1. What is ab initio?
Blinded docking or ab initio is the protocol to execute when no additional information is provided for performing the docking (residue restraints, etc.).
Default recommended protocol is:
- Swarms: 400
- Glowworms: 300
- Steps: 100
In the original publication the number of steps was equal to 200, but quality of the results is not affected using 100 steps. The reason behind performing 200 steps was for benchmarking the method.
2.1. Removing previous files when setup fails
If LightDock setup fails and no
setup.json file is generated, all files generated by LightDock should be deleted. This is critical as LightDock may append PDB structures parsed to
lightdock_*.pdb existing PDB files, with the result of multiple structures per PDB file.
3.1. DFIRE fails with KeyError
DFIRE scoring function fails with a similar error to this example:
File "/home/software/lightdock/lightdock/scoring/dfire/driver.py", line 152, in _get_docking_model anuma = atomnumber[rec_atom_type] KeyError: 'LYSH1'
This is caused by DFIRE scoring functions not recognizing
H (hydrogen) atoms. Remove all hydrogen atoms and any other non-standard residue or
For removing hydrogens, you can use the flag
lightdock_setup command or the Reduce software:
reduce -Trim input.pdb > output.pdb