The adfr command is used to dock a ligand into a receptor modelled by a given target file.
> adfr -l 3c9w_ligandWithSideChain_random.pdbqt # ligand
-t 3c9w_cov_cmdline.trg # receptor
-C 1 2 3 # ligand pdb serial numbers of covalent attachment atoms
--jobName covalent # name for this docking calculation
--nbRuns 8 # limit the number of GA evolutions for quick demo
--maxEvals 20000 # limit number of evals for quick demo
--seed 1 # a known seed makes the output is predictable
-O # over write output files if they exist
the full output of this command is available here.
The ligand to dock is specified using the Ðl/--ligand command line option. This option is required.
The receptor and the pocket into which to dock is specified using the Ðt/--target command line option. This target file contains the covaklent attachment definition on the receptor side.
The 3 atoms defining the ligand atoms overlapping with the 3 receptor atoms defining the covalent attachment point are specified using the ÐC/--covalenLigand option.
This docking run is called ÒcovalentÓ (-J/--jobName). The files produced by this run are named using the ligand name and the jobname:
3c9w_ligandWithSideChain_random_covalent_out.pdbqt # solutions, multi-model pdbqt file
3c9w_ligandWithSideChain_random_covalent_summary.dlg # log file
3c9w_ligandWithSideChain_random_covalent.dro # Docking Result Object (.dro) file
the remaining options in this example are used to make the calculation short for demonstration purposes (ÐmaxEvals ÐnbRuns), make the results predictable (Ðseed) and prevent the program from stopping if output files already exist (-O)
Each one of the 8 evolutions produce a docking pose. These 8 poses are clustered and the solution with the best free energy of binding (not docking score) are reported as docking solutions. These solution are store in the 3c9w_ligandWithSideChain_random_covalent_out.pdbqt multi-model pdbqt file.
The log file 3c9w_ligandWithSideChain_random_covalent_summary.dlg captures the messages printed to the screen during the calculation and provides more detailed clustering information.
The 3c9w_ligandWithSideChain_random_covalent.dro file contains all input and results from the docking calculations. This file can be opened using Pmv or inspected using the about command. containing the following information structured as a file system: