FAQ: Frequently Asked Questions

Table of Contents

1. General

1.1. What is ab initio?

Blind 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: 200
  • 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. Setup

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. Simulation

3.1. DFIRE fails with KeyError

In old versions of LightDock and when using DFIRE scoring function, lightdock might fail 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 HETATM.

For removing hydrogens, you can use the flag --noh in lightdock_setup command or the Reduce software:

reduce -Trim input.pdb > output.pdb

Other scoring functions might fail for similar reasons.