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.).

By default LightDock setup considers:

  • Number of Swarms: 400
  • Number of Glowworms: 200

About the number of steps, in the original publication the number of steps was equal to 200, but quality of the results is not affected if using 100 steps. The reason behind performing 200 steps was for benchmarking the method.

We recommend using 100 steps of simulation.

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. Remove all the generated files by LightDock and leave only the original input to perform a new setup.

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

DFIRE scoring function (dfire, fastdfire) only recognizes the 20 standard aminoacids (other scoring functions might fail for similar reasons).