### LightDock Setup Output Example Source: https://lightdock.org/tutorials/0.9.3/membrane This output shows the typical log messages during the LightDock setup process, including warnings about incomplete sidechains and confirmation of file processing. ```text [lightdock3_setup] INFO: Ignoring OXT atoms [lightdock3_setup] INFO: Ignoring Hydrogen atoms [lightdock3_setup] INFO: Reading structure from 3x29_receptor_membrane.pdb PDB file... [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue GLN.61 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue GLN.63 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue LYS.65 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue LEU.66 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue ASP.68 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue HIS.76 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue MET.95 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue MET.102 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue LYS.103 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue LYS.115 [pdb] WARNING: Possible problem: [SideChainError] Incomplete sidechain for residue ARG.117 [lightdock3_setup] INFO: 1608 atoms, 601 residues read. [lightdock3_setup] INFO: Ignoring OXT atoms [lightdock3_setup] INFO: Ignoring Hydrogen atoms [lightdock3_setup] INFO: Reading structure from 3x29_ligand.pdb PDB file... [lightdock3_setup] INFO: 933 atoms, 117 residues read. [lightdock3_setup] INFO: Calculating reference points for receptor 3x29_receptor_membrane.pdb... [lightdock3_setup] INFO: Reference points for receptor found, skipping [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Calculating reference points for ligand 3x29_ligand.pdb... [lightdock3_setup] INFO: Reference points for ligand found, skipping [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Saving processed structure to PDB file... [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Saving processed structure to PDB file... [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Calculating starting positions... [lightdock3_setup] INFO: Generated 62 positions files [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Number of calculated swarms is 62 [lightdock3_setup] INFO: Preparing environment [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: LightDock setup OK ``` -------------------------------- ### LightDock Setup Output Example Source: https://lightdock.org/tutorials/0.9.3/restraints This output shows the successful execution of the LightDock setup, including reading structures, calculating reference points, processing restraints, and generating initial swarm positions. ```text @> ProDy is configured: verbosity='info' [lightdock_setup] INFO: Reading structure from 4G6M_rec.pdb PDB file... [lightdock_setup] INFO: 1782 atoms, 230 residues read. [lightdock_setup] INFO: Reading structure from 4G6M_lig.pdb PDB file... [lightdock_setup] INFO: 1194 atoms, 149 residues read. [lightdock_setup] INFO: Calculating reference points for receptor 4G6M_rec.pdb... [lightdock_setup] INFO: Done. [lightdock_setup] INFO: Calculating reference points for ligand 4G6M_lig.pdb... [lightdock_setup] INFO: Done. [lightdock_setup] INFO: Saving processed structure to PDB file... [lightdock_setup] INFO: Done. [lightdock_setup] INFO: Saving processed structure to PDB file... [lightdock_setup] INFO: Done. [lightdock_setup] INFO: 10 normal modes calculated [lightdock_setup] INFO: 10 normal modes calculated [lightdock_setup] INFO: Reading restraints from restraints.list [lightdock_setup] INFO: Number of receptor restraints is: 20 (active), 0 (passive) [lightdock_setup] INFO: Number of ligand restraints is: 21 (active), 0 (passive) [lightdock_setup] INFO: Calculating starting positions... [lightdock_setup] INFO: Generated 55 positions files [lightdock_setup] INFO: Done. [lightdock_setup] INFO: Number of swarms is 55 after applying restraints [lightdock_setup] INFO: Preparing environment [lightdock_setup] INFO: Done. [lightdock_setup] INFO: LightDock setup OK ``` -------------------------------- ### Run LightDock Rust Docking Simulation Source: https://lightdock.org/tutorials/0.9.3/rust Execute a real docking example using the lightdock-rust binary. This command initiates a docking simulation from a specified setup file. ```bash cd example/1ppe time ../../target/release/lightdock-rust setup_1ppe.json initial_positions_0.dat 100 dfire ``` -------------------------------- ### LightDock Setup Command Help Source: https://lightdock.org/tutorials/0.9.3/simple_docking Displays the usage information for the `lightdock3_setup` command, outlining available arguments and options. ```bash usage: lightdock3_setup [-h] [-s SWARMS] [-g GLOWWORMS] [--seed_points STARTING_POINTS_SEED] [--noxt] [--noh] [--now] [--verbose_parser] [-anm] [--seed_anm ANM_SEED] [--anm_rec_rmsd ANM_REC_RMSD] [--anm_lig_rmsd ANM_LIG_RMSD] [-ar ANM_REC] [-al ANM_LIG] [-r restraints] [-membrane] [-transmembrane] [-sp] [-sd SURFACE_DENSITY] [-sr SWARM_RADIUS] [-flip] [-fd FIXED_DISTANCE] [-spr SWARMS_PER_RESTRAINT] [--ds] [-V] receptor_pdb_file ligand_pdb_file lightdock3_setup: error: the following arguments are required: receptor_pdb_file, ligand_pdb_file ``` -------------------------------- ### LightDock Setup Output Source: https://lightdock.org/tutorials/0.9.3/dna_docking This is the expected output when the `lightdock3_setup.py` script runs successfully. It confirms the reading of structures, calculation of reference points, ANM, and restraints, and the generation of starting positions. ```text @> ProDy is configured: verbosity='none' [lightdock3_setup] INFO: Reading structure from protein.pdb PDB file... [lightdock3_setup] INFO: 1094 atoms, 66 residues read. [lightdock3_setup] INFO: Reading structure from dna.pdb PDB file... [lightdock3_setup] INFO: 506 atoms, 16 residues read. [lightdock3_setup] INFO: Calculating reference points for receptor protein.pdb... [lightdock3_setup] INFO: Reference points for receptor found, skipping [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Calculating reference points for ligand dna.pdb... [lightdock3_setup] INFO: Reference points for ligand found, skipping [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Saving processed structure to PDB file... [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Saving processed structure to PDB file... [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Calculating ANM for receptor molecule... [lightdock3_setup] INFO: 10 normal modes calculated [lightdock3_setup] INFO: Calculating ANM for ligand molecule... [lightdock3_setup] INFO: 10 normal modes calculated [lightdock3_setup] INFO: Reading restraints from restraints.list [lightdock3_setup] INFO: Number of receptor restraints is: 3 (active), 0 (passive) [lightdock3_setup] INFO: Number of ligand restraints is: 0 (active), 0 (passive) [lightdock3_setup] INFO: Calculating starting positions... [lightdock3_setup] INFO: Generated 21 positions files [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: Number of calculated swarms is 21 [lightdock3_setup] INFO: Preparing environment [lightdock3_setup] INFO: Done. [lightdock3_setup] INFO: LightDock setup OK ``` -------------------------------- ### Install Rust Environment with rustup Source: https://lightdock.org/tutorials/0.9.3/rust Use this command to install the Rust compiler and cargo package manager. Follow the instructions on the rustup website for detailed setup. ```bash curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh ``` -------------------------------- ### Run LightDock Setup Script Source: https://lightdock.org/tutorials/0.9.3/dna_docking Execute the setup script with protein and DNA PDB files, enabling ANM and restraints. Ensure the restraints file is correctly specified. ```bash lightdock3_setup.py protein.pdb dna.pdb -anm -rst restraints.list ``` -------------------------------- ### LightDock Simulation Output Example Source: https://lightdock.org/tutorials/0.9.3/simple_docking Shows the typical output generated during a LightDock simulation, including setup information, progress of steps, and completion messages. This helps in monitoring the simulation's progress. ```text @> ProDy is configured: verbosity='info' [lightdock3_setup] INFO: Ignoring OXT atoms [lightdock3_setup] INFO: Ignoring Hydrogen atoms [lightdock3_setup] INFO: Ignoring water [lightdock3_setup] INFO: Reading structure from lightdock_2UUY_rec.pdb PDB file... [lightdock3_setup] INFO: 1628 atoms, 223 residues read. [lightdock3_setup] INFO: Ignoring OXT atoms [lightdock3_setup] INFO: Ignoring Hydrogen atoms [lightdock3_setup] INFO: Ignoring water [lightdock3_setup] INFO: Reading structure from lightdock_2UUY_lig.pdb PDB file... [lightdock3_setup] INFO: 415 atoms, 55 residues read. [lightdock] INFO: Loading scoring function... [lightdock] INFO: Using DFIRE scoring function [lightdock] INFO: Done. [kraken] INFO: Kraken has 1 tentacles (cpu cores) [kraken] INFO: Tentacle ready with 1 tasks [kraken] INFO: 1 ships ready to be smashed [lightdock] INFO: Monster spotted [kraken] INFO: Release the Kraken! [0] step 1 [0] step 2 [0] step 3 [0] step 4 [0] step 5 [0] step 6 [0] step 7 [0] step 8 [0] step 9 [0] step 10 ... [0] step 100 [kraken] INFO: folding tentacle Tentacle-1 [kraken] INFO: 1 ships destroyed [lightdock] INFO: Finished. ``` -------------------------------- ### Run LightDock Setup with Restraints Source: https://lightdock.org/tutorials/0.9.3/restraints Execute the setup script with receptor and ligand PDB files, specifying options to exclude terminal oxygens, hydrogens, and water, enable normal modes, and apply residue restraints from a list. ```bash lightdock3_setup.py 4G6M_rec.pdb 4G6M_lig.pdb --noxt --noh --now -anm -rst restraints.list ``` -------------------------------- ### LightDock Setup Command Usage Source: https://lightdock.org/tutorials/0.9.3/membrane This shows the usage information for the `lightdock3_setup` command, including required arguments and available optional flags for customization. ```text usage: lightdock3_setup [-h] [-s SWARMS] [-g GLOWWORMS] [--seed_points STARTING_POINTS_SEED] [--noxt] [--noh] [--verbose_parser] [-anm] [--seed_anm ANM_SEED] [-ar ANM_REC] [-al ANM_LIG] [-r restraints] [-membrane] [-transmembrane] [-sp] [-sd SURFACE_DENSITY] [-sr SWARM_RADIUS] receptor_pdb_file ligand_pdb_file lightdock3_setup: error: the following arguments are required: receptor_pdb_file, ligand_pdb_file ``` -------------------------------- ### LightDock Setup Command-Line Interface Source: https://lightdock.org/tutorials/0.9.3/basics This snippet shows the usage and required arguments for the `lightdock3_setup.py` script. It highlights the mandatory receptor and ligand PDB file inputs. ```bash usage: lightdock3_setup [-h] [-s SWARMS] [-g GLOWWORMS] [--seed_points STARTING_POINTS_SEED] [--noxt] [--noh] [--now] [--verbose_parser] [-anm] [--seed_anm ANM_SEED] [--anm_rec_rmsd ANM_REC_RMSD] [--anm_lig_rmsd ANM_LIG_RMSD] [-ar ANM_REC] [-al ANM_LIG] [-r restraints] [-membrane] [-transmembrane] [-sp] [-sd SURFACE_DENSITY] [-sr SWARM_RADIUS] [-flip] [-fd FIXED_DISTANCE] [-spr SWARMS_PER_RESTRAINT] [--ds] receptor_pdb_file ligand_pdb_file lightdock3_setup: error: the following arguments are required: receptor_pdb_file, ligand_pdb_file ``` -------------------------------- ### Run LightDock Setup Script Source: https://lightdock.org/tutorials/0.9.3/rna_docking Execute the setup script for LightDock, specifying the protein and RNA PDB files. This command enables the calculation of normal modes (ANM) for both molecules. ```bash lightdock3_setup.py protein.pdb rna.pdb -anm ``` -------------------------------- ### Install LightDock Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb Installs the LightDock package and its dependencies. Ensure you are using version 0.9.0 as specified. ```bash !pip install lightdock==0.9.0 ``` ```bash !pip install pdb-tools ``` ```bash !pip install py3dmol ``` -------------------------------- ### Setup LightDock for Membrane Simulation Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb Prepares the PDB files for LightDock simulation, specifying membrane environment and disabling certain options. ```bash !lightdock3_setup.py 3x29_receptor_membrane.pdb 3x29_ligand.pdb --noxt --noh --membrane ``` -------------------------------- ### Basic LightDock Simulation Execution Source: https://lightdock.org/tutorials/0.9.3/basics The simplest way to run a LightDock simulation, requiring only the setup file and the number of simulation steps. ```bash lightdock3.py setup.json 10 ``` -------------------------------- ### Basic LightDock Setup Command Source: https://lightdock.org/tutorials/0.9.3/simple_docking Executes the `lightdock3_setup.py` script with essential arguments for receptor and ligand PDB files, along with flags to exclude OXT atoms, hydrogens, waters, and enable ANM support. ```bash lightdock3_setup.py 2UUY_rec.pdb 2UUY_lig.pdb --noxt --noh --now -anm ``` -------------------------------- ### Verify LightDock Installation Source: https://lightdock.org/tutorials/0.9.3/membrane Check if LightDock is installed correctly by running the version command in the terminal. ```bash lightdock3.py -v ``` -------------------------------- ### Running a Basic LightDock Simulation Source: https://lightdock.org/tutorials/0.9.3/simple_docking Executes a LightDock simulation with a specified setup file, number of steps, and number of CPU cores. This is a common command for initiating a docking process. ```bash lightdock3.py setup.json 100 -c 1 -l 0 ``` -------------------------------- ### Execute the Simulation Script Source: https://lightdock.org/tutorials/0.9.3/rust Run the prepared execution script to start the lightdock-rust simulations. Ensure NUM_CORES is set appropriately in the script. ```bash ./execution.sh ``` -------------------------------- ### Install LightDock via pip Source: https://lightdock.org/tutorials/0.9.3/membrane Install LightDock version 0.9.3.post1 using pip within a virtual environment. Ensure Python 3.6+ is used. ```bash virtualenv venv source venv/bin/activate pip install lightdock==0.9.3.post1 ``` -------------------------------- ### Run LightDock3 Setup for 1CZY Complex Source: https://lightdock.org/tutorials/0.9.3/rust Execute the lightdock3_setup.py script to prepare the docking simulation for the 1CZY complex using the downloaded PDB and restraint files. This generates the necessary input for the lightdock-rust binary. ```bash lightdock3_setup.py 1czy_protein.pdb 1czy_peptide.pdb --noxt --noh -anm -rst restraints.list -spr 10 ``` -------------------------------- ### Install LightDock in Jupyter/Colab Source: https://lightdock.org/tutorials/0.9.3/membrane Install LightDock version 0.9.3.post1 using pip in a Jupyter Notebook or Google Colab environment. ```python !pip install lightdock==0.9.3.post1 ``` -------------------------------- ### GSO Configuration File Example Source: https://lightdock.org/tutorials/0.9.3/basics An example of a GlowWorm Swarm Optimization (GSO) configuration file, detailing parameters like rho, gamma, and initial Luciferin. Advanced users can modify these for custom simulations. ```ini ## # # GlowWorm configuration file - algorithm parameters # ## [GSO] # Rho rho = 0.4 # Gamma gamma = 0.6 # Initial Luciferin initialLuciferin = 5.0 # Initial glowworm vision range (in A) initialVisionRange = 15.0 # Max vision range (in A) maximumVisionRange = 40.0 # Beta beta = 0.16 # Max number of neighbors maximumNeighbors = 5 ``` -------------------------------- ### Example LightDock Output Line Source: https://lightdock.org/tutorials/0.9.3/simple_docking An example line from a LightDock output file, detailing coordinates, IDs, scoring, and other parameters for a glowworm agent. ```text #Coordinates RecID LigID Luciferin Neighbor's number Vision Range Scoring ( 8.3619938, -9.0568297, -23.0839562, -0.6368250, -0.1214085, 0.4488531, -0.6150161, 5.2922640, 4.6293871, 5.1679589, 3.6238049, 3.9717360, 7.2390017, 4.5821031, 5.4562578, 1.9734713, 2.9626742, 1.0323748, 5.8207747, 3.4377706, 2.6552282, 4.8705878, 3.0931470, 3.4670304, 3.9487060, 2.4948334, 4.5626560) 0 0 27.83190014 6 0.320 18.65982945 ``` -------------------------------- ### Run LightDock Simulation Source: https://lightdock.org/tutorials/0.9.3/membrane Execute the LightDock simulation using a setup file, specifying simulation steps, CPU cores, scoring function, and optionally a specific swarm to run. ```bash lightdock3.py setup.json 100 -c 1 -s fastdfire -l 60 ``` -------------------------------- ### Run LightDock Simulation Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb Executes a LightDock simulation using a setup file, specifying swarm size, number of clusters, and search algorithm. ```bash !lightdock3.py setup.json 100 -c 1 -s fastdfire -l 60 ``` -------------------------------- ### Install PDB-Tools in Jupyter/Colab Source: https://lightdock.org/tutorials/0.9.3/membrane Install the PDB-Tools package using pip within a Jupyter Notebook or Google Colab environment. ```python !pip install pdb-tools ``` -------------------------------- ### Run Lightdock-Rust Simulation Source: https://lightdock.org/tutorials/0.9.3/rust Execute the lightdock-rust binary to simulate the first swarm. This command requires a setup JSON file, initial positions, number of steps, and a scoring function. ```bash time ../../target/release/lightdock-rust setup.json init/initial_positions_0.dat 100 dfire ``` -------------------------------- ### LightDock Model Generation Log Source: https://lightdock.org/tutorials/0.9.3/simple_docking Example log output from the 'lgd_generate_conformations.py' script, showing the progress of reading PDB files and generating conformations. ```text [generate_conformations] INFO: Reading ../lightdock_2UUY_rec.pdb receptor PDB file... [generate_conformations] INFO: 1628 atoms, 223 residues read. [generate_conformations] INFO: Reading ../lightdock_2UUY_lig.pdb ligand PDB file... [generate_conformations] INFO: 415 atoms, 55 residues read. [generate_conformations] INFO: Read 200 coordinate lines [generate_conformations] INFO: Generated 200 conformations ``` -------------------------------- ### View LightDock Output Header Source: https://lightdock.org/tutorials/0.9.3/simple_docking Use the 'head' command to display the first few lines of a LightDock output file, showing the header and an example data line. ```bash head -2 swarm_0/gso_100.out ``` -------------------------------- ### Install PDB-Tools via pip Source: https://lightdock.org/tutorials/0.9.3/membrane Install the PDB-Tools package using pip. This package provides scripts for manipulating PDB files. ```bash pip install pdb-tools ``` -------------------------------- ### Command to Remove Generated Files Source: https://lightdock.org/tutorials/0.9.3/simple_docking A utility command to clean up all files and directories generated by the LightDock setup process, useful for retrying the setup if it fails. ```bash rm -rf lightdock* setup.json init/ swarm_* ``` -------------------------------- ### LightDock Command-Line Usage Source: https://lightdock.org/tutorials/0.9.3/basics Displays the accepted command-line options when `lightdock3` is executed without arguments. This helps in understanding the available parameters for simulation setup. ```bash usage: lightdock3 [-h] [-f configuration_file] [-s SCORING_FUNCTION] [-sg GSO_SEED] [-t TRANSLATION_STEP] [-r ROTATION_STEP] [-V] [-c CORES] [--profile] [-mpi] [-ns NMODES_STEP] [-min] [--listscoring] [-l SWARM_LIST [SWARM_LIST ...]] setup_file steps lightdock3: error: the following arguments are required: setup_file, steps ``` -------------------------------- ### Parallelize Lightdock Execution with ant_thony.py Source: https://lightdock.org/tutorials/0.9.3/rust This script automates the setup, data conversion, and execution of lightdock-rust simulations in parallel using ant_thony.py. Adjust NUM_CORES to match your system's CPU cores. ```bash #!/bin/bash # Edit only the number of cores to use for this simulation NUM_CORES=4 # LightDock setup lightdock3_setup.py 1czy_protein.pdb 1czy_peptide.pdb --noxt --noh -anm -rst restraints.list -spr 10 # Convert ANM data lgd_flatten.py lightdock_rec.nm.npy rec_nm.npy lgd_flatten.py lightdock_lig.nm.npy lig_nm.npy # Calculate number of swarms s=`ls -d swarm_* | wc -l` swarms=$((s-1)) # Copy lightdock-rust binary cp ../../target/release/lightdock-rust . # Create a task.list file for ant_thony for i in `seq 0 $swarms`;do echo "./lightdock-rust setup.json init/initial_positions_${i}.dat 100 dfire;" >> task.list; done # Let ant_thony run time ant_thony.py --cores ${NUM_CORES} task.list # Clean task.list rm -rf task.list ``` -------------------------------- ### Visualize Swarm Centers with PyMOL Source: https://lightdock.org/tutorials/0.9.3/membrane This command visualizes the distribution of swarm centers over the receptor structure using PyMOL. It requires the receptor PDB file and the swarm centers file generated during setup. ```bash pymol lightdock_3x29_receptor_membrane.pdb init/swarm_centers.pdb ``` -------------------------------- ### Run Local RNA Docking Simulation Source: https://lightdock.org/tutorials/0.9.3/rna_docking Execute a local RNA docking simulation using LightDock. Specify the setup file, number of steps, scoring function, and number of CPU cores. ```bash lightdock3.py setup.json 100 -s dna -c 8 ``` -------------------------------- ### Download Data for 1CZY Complex Docking Source: https://lightdock.org/tutorials/0.9.3/rust Download necessary PDB and restraint files for performing a docking simulation on the 1CZY complex. These files are required for the setup process. ```bash mkdir 1czy cd 1czy wget https://raw.githubusercontent.com/lightdock/lightdock-rust/master/example/1czy/1czy_protein.pdb wget https://raw.githubusercontent.com/lightdock/lightdock-rust/master/example/1czy/1czy_peptide.pdb wget https://raw.githubusercontent.com/lightdock/lightdock-rust/master/example/1czy/restraints.list ``` -------------------------------- ### Example Residue Restraints Source: https://lightdock.org/tutorials/0.9.3/dna_docking This snippet shows the format of residue restraints within the 'restraints.list' file. It specifies restraints on the receptor (protein partner) at specific residues. ```text R A.TRP.24 R A.VAL.26 R A.ARG.42 ``` -------------------------------- ### Download Residue Restraints List Source: https://lightdock.org/tutorials/0.9.3/dna_docking Download the predefined 'restraints.list' file, which specifies residue restraints to guide the docking process. This file is crucial for incorporating experimental or bioinformatic information. ```bash curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/restraints.list ``` -------------------------------- ### Generated setup.json Configuration Source: https://lightdock.org/tutorials/0.9.3/simple_docking The `setup.json` file contains all parameters used for the LightDock simulation, useful for reproducibility and parameter verification. Avoid modifying this file unless you are certain of the implications. ```json { "anm_lig": 10, "anm_rec": 10, "anm_seed": 324324, "flip": false, "glowworms": 200, "ligand_pdb": "2UUY_lig.pdb", "membrane": false, "noh": true, "now": true, "noxt": true, "receptor_pdb": "2UUY_rec.pdb", "restraints": null, "starting_points_seed": 324324, "surface_density": 50.0, "swarm_radius": 10.0, "swarms": 182, "transmembrane": false, "use_anm": true, "verbose_parser": false, "write_starting_positions": false } ``` -------------------------------- ### Set up LightDock Membrane Simulation Source: https://lightdock.org/tutorials/0.9.3/membrane Use this command to initialize a membrane simulation with specified receptor and ligand PDB files. Flags `--noxt` and `--noh` are used to ignore OXT and hydrogen atoms, respectively. ```bash lightdock3_setup.py 3x29_receptor_membrane.pdb 3x29_ligand.pdb --noxt --noh --membrane ``` -------------------------------- ### DFIRE KeyError Example Source: https://lightdock.org/tutorials/0.9.3/faq This is an example of a KeyError that may occur with DFIRE scoring functions in older LightDock versions due to unrecognized atom types. It indicates that DFIRE does not recognize certain atom types, such as those in HETATM records or non-standard residues. ```python File "/home/software/lightdock/lightdock/scoring/dfire/driver.py", line 152, in _get_docking_model anuma = atomnumber[rec_atom_type] KeyError: 'LYSH1' ``` -------------------------------- ### LightDock Simulation Command Help Source: https://lightdock.org/tutorials/0.9.3/simple_docking Displays the usage information and available arguments for the `lightdock3` command. Use this to understand all possible simulation configurations. ```bash usage: lightdock3 [-h] [-f configuration_file] [-s SCORING_FUNCTION] [-sg GSO_SEED] [-t TRANSLATION_STEP] [-r ROTATION_STEP] [-V] [-c CORES] [--profile] [-mpi] [-ns NMODES_STEP] [-min] [--listscoring] [-l SWARM_LIST [SWARM_LIST ...]] setup_file steps lightdock3: error: the following arguments are required: setup_file, steps ``` -------------------------------- ### Download Sample Data for 1AZP Complex Source: https://lightdock.org/tutorials/0.9.3/dna_docking Create a directory and download the necessary PDB files for the 1AZP protein-DNA complex. This is the initial step for setting up the docking simulation. ```bash mkdir 1azp cd 1azp curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/1AZP_A.pdb curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/dna_docking/data/1AZP_B.pdb ``` -------------------------------- ### Download Sample Data for Docking Source: https://lightdock.org/tutorials/0.9.3/simple_docking Use these commands to create a working directory and download the receptor and ligand PDB files required for the docking simulation. ```bash mkdir test cd test curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/simple_docking/data/2UUY_rec.pdb curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/simple_docking/data/2UUY_lig.pdb ``` -------------------------------- ### Download Sample Data Source: https://lightdock.org/tutorials/0.9.3/rna_docking Create a directory and download the necessary PDB files for the 1A1T protein-RNA complex. ```bash mkdir 1a1t cd 1a1t curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/rna_docking/data/1A1T_A.pdb curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/rna_docking/data/1A1T_B.pdb ``` -------------------------------- ### Open Receptor and Membrane in PyMOL Source: https://lightdock.org/tutorials/0.9.3/membrane Launch PyMOL with both the atomistic receptor PDB and the processed coarse-grained membrane PDB files to prepare for alignment. ```bash pymol 3x29_receptor.pdb membrane_cg.pdb ``` -------------------------------- ### Run Local Simulation with LightDock Source: https://lightdock.org/tutorials/0.9.3/restraints Execute a LightDock simulation on a local machine using specified parameters. This command simulates 55 swarms with 100 steps each, using the fastDFIRE scoring function and 8 CPU cores. ```bash lightdock3.py setup.json 100 -s fastdfire -c 8 ``` -------------------------------- ### Compile LightDock-Rust from Source Source: https://lightdock.org/tutorials/0.9.3/rust Clone the repository and build the release version of the LightDock-Rust binary. The compiled executable will be located in the target/release directory. ```bash git clone https://github.com/lightdock/lightdock-rust cd lightdock-rust cargo build --release ``` -------------------------------- ### Simulate Single Swarm with LightDock Source: https://lightdock.org/tutorials/0.9.3/restraints Run a LightDock simulation for a specific swarm (ID=0) with limited resources. This command uses 1 core and simulates 100 steps for the first swarm. ```bash lightdock3.py setup.json 100 -c 1 -l 0 ``` -------------------------------- ### Download Sample Data for Docking Source: https://lightdock.org/tutorials/0.9.3/restraints Use these curl commands to download the receptor and ligand PDB files for the 4G6M protein complex. Ensure you are in the correct directory before running. ```bash mkdir test cd test curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/restraints/data/4G6M_rec.pdb curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/restraints/data/4G6M_lig.pdb ``` -------------------------------- ### Display LightDock Rust Command-Line Usage Source: https://lightdock.org/tutorials/0.9.3/rust Execute the lightdock-rust binary without arguments to display its usage instructions and required parameters. ```bash ./target/release/lightdock-rust Wrong command line. Usage: ./target/release/lightdock-rust setup_filename swarm_filename steps method ``` -------------------------------- ### View Prediction Summary File Source: https://lightdock.org/tutorials/0.9.3/rna_docking Display the beginning of the 'solutions.list' file to inspect the summary of predicted structures, including swarm, glowworm, scores, and PDB file names. ```bash head solutions.list ``` -------------------------------- ### Protein Protonation with Reduce Source: https://lightdock.org/tutorials/0.9.3/rna_docking Prepare the protein PDB file by removing existing hydrogens and rebuilding them using the 'reduce' software for AMBER94 force-field compatibility. ```bash reduce -Trim 1A1T_A.pdb > 1A1T_A_noh.pdb reduce -BUILD 1A1T_A_noh.pdb > 1A1T_A_h.pdb ``` -------------------------------- ### RNA Protonation with Reduce Source: https://lightdock.org/tutorials/0.9.3/rna_docking Prepare the RNA PDB file by removing existing hydrogens and rebuilding them using the 'reduce' software. ```bash reduce -Trim 1A1T_B.pdb > 1A1T_B_noh.pdb reduce -BUILD 1A1T_B_noh.pdb > 1A1T_B_h.pdb ``` -------------------------------- ### Visualize Ligand PDB with py3Dmol Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb Loads and visualizes the ligand PDB file in a 3D viewer. ```python import py3Dmol with open("3x29_ligand.pdb") as ifile: ligand = "".join([x for x in ifile]) view = py3Dmol.view(width=600, height=600) view.addModelsAsFrames(ligand) view.setStyle({'model': -1}, {"cartoon": {'color': 'spectrum'}}) view.zoomTo() view.show() ``` -------------------------------- ### Generate Docking Conformations Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb Generates a specified number of conformations from the LightDock simulation output. ```bash !lgd_generate_conformations.py 3x29_receptor_membrane.pdb 3x29_ligand.pdb swarm_60/gso_100.out 200 ``` -------------------------------- ### Generate Conformations with lgd_generate_conformations.py Source: https://lightdock.org/tutorials/0.9.3/membrane Generate predicted models from simulation output files. This script requires the receptor and ligand PDB files, the simulation output file, and the number of conformations to generate. ```bash lgd_generate_conformations.py 3x29_receptor_membrane.pdb 3x29_ligand.pdb swarm_60/gso_100.out 200 ``` -------------------------------- ### HPC Post-processing PBS Script Source: https://lightdock.org/tutorials/0.9.3/dna_docking A comprehensive PBS script for post-processing LightDock simulation results on an HPC cluster. It includes steps for generating conformations, clustering, ranking, and filtering. ```bash #PBS -N 1AZP-post #PBS -q medium #PBS -l nodes=1:ppn=8 #PBS -S /bin/bash #PBS -d ./ #PBS -e ./postprocessing.err #PBS -o ./postprocessing.out ### Calculate the number of swarms ### s=`ls -d ./swarm_* | wc -l` swarms=$((s-1)) ### Create files for Ant-Thony ### for i in $(seq 0 $swarms) do echo "cd swarm_${i}; lgd_generate_conformations.py ../protein.pdb ../dna.pdb gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list; done for i in $(seq 0 $swarms) do echo "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list; done ### Generate LightDock models ### ant_thony.py -c 8 generate_lightdock.list; ### Clustering BSAS (rmsd) within swarm ### ant_thony.py -c 8 cluster_lightdock.list; ### Generate ranking files for filtering ### lgd_rank.py $s 100; ### Filtering models by >40% of satisfied restraints ### lgd_filter_restraints.py --cutoff 5.0 --fnat 0.4 -lnuc rank_by_scoring.list restraints.list A B ``` -------------------------------- ### Download Pre-formatted Restraint List Source: https://lightdock.org/tutorials/0.9.3/restraints Download a pre-formatted 'restraints.list' file using curl. This file contains residue restraints ready for use in LightDock. ```bash curl -O https://raw.githubusercontent.com/lightdock/lightdock.github.io/master/tutorials/0.9.3/restraints/data/restraints.list ``` -------------------------------- ### Full LightDock Analysis Protocol Source: https://lightdock.org/tutorials/0.9.3/restraints A comprehensive PBS script that automates the entire LightDock analysis workflow, including structure generation, intra-swarm clustering, ranking, and restraint-based filtering. It is designed for execution on an HPC cluster. ```bash #PBS -N 4G6M-anal #PBS -q medium #PBS -l nodes=1:ppn=8 #PBS -S /bin/bash #PBS -d ./ #PBS -e ./analysis.err #PBS -o ./analysis.out CORES=8 ### Calculate the number of swarms ### s=`ls -d ./swarm_* | wc -l` swarms=$((s-1)) ### Create files for Ant-Thony ### for i in $(seq 0 $swarms) do echo "cd swarm_${i}; lgd_generate_conformations.py ../4G6M_rec.pdb ../4G6M_lig.pdb gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list; done for i in $(seq 0 $swarms) do echo "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list; done ### Generate LightDock models ### ant_thony.py -c ${CORES} generate_lightdock.list; ### Clustering BSAS (rmsd) within swarm ### ant_thony.py -c ${CORES} cluster_lightdock.list; ### Generate ranking files for filtering ### lgd_rank.py $s 100; ### Filtering models by >40% of satisfied restraints ### lgd_filter_restraints.py --cutoff 5.0 --fnat 0.4 rank_by_scoring.list restraints.list A B > /dev/null 2> /dev/null; ``` -------------------------------- ### Open Structures in PyMOL Source: https://lightdock.org/tutorials/0.9.3/membrane Opens the target docking model and the reference structure in PyMOL for visualization and analysis. Ensure both PDB files are in the current directory. ```bash pymol swarm_22_112.pdb 3x29_reference.pdb ``` -------------------------------- ### Generate Predicted Docked Models Source: https://lightdock.org/tutorials/0.9.3/simple_docking Use the 'lgd_generate_conformations.py' script to create PDB files for docked structures. Provide receptor, ligand, LightDock output, and the number of conformations to generate. ```bash cd swarm_0 lgd_generate_conformations.py ../2UUY_rec.pdb ../2UUY_lig.pdb gso_100.out 200 ``` -------------------------------- ### Visualize Top Models with py3Dmol Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb Use this snippet to load a PDB file, add its models to a py3Dmol viewer, apply custom styles to chains and residues, and display the visualization. Ensure the PDB file exists at the specified path. ```python import py3Dmol with open("swarm_60/lightdock_115.pdb") as ifile: structure = "".join([x for x in ifile]) view = py3Dmol.view(width=600, height=600) view.addModelsAsFrames(structure) view.setStyle({'chain': 'A'}, {"cartoon": {'color': 'blue'}}) view.setStyle({'chain': 'B'}, {"cartoon": {'color': 'green'}}) view.setStyle({'resn':'MMB'}, {"sphere": {'color': 'orange'}}) view.zoomTo() view.show() ``` -------------------------------- ### Prepare Membrane PDB for LightDock Source: https://lightdock.org/tutorials/0.9.3/membrane Execute this Python script to parse, rename, and filter beads from a coarse-grained PDB file for membrane simulations in LightDock. Ensure the input PDB file is correctly named. ```bash python3 prepare4lightdock.py 3x29_default_dppc-coarsegrained.pdb membrane_cg.pdb ``` -------------------------------- ### Generate Predicted Models with lgd_generate_conformations.py Source: https://lightdock.org/tutorials/0.9.3/basics Use this command to generate PDB structure files for predicted models after a simulation. Ensure you provide the receptor structure, ligand structure, LightDock output file, and the number of glowworms. ```bash usage: conformer_conformations [-h] [--setup setup_file] receptor_structure ligand_structure lightdock_output glowworms conformer_conformations: error: the following arguments are required: receptor_structure, ligand_structure, lightdock_output, glowworms ``` ```bash cd $LIGHTDOCK_HOME/examples/2UUY cd swarm_0 lgd_generate_conformations.py ../2UUY_rec.pdb ../2UUY_lig.pdb gso_5.out 10 ``` -------------------------------- ### Cluster Docking Models Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb Clusters the generated docking models based on their Binding Site Similarity (BSS). ```bash !lgd_cluster_bsas.py swarm_60/gso_100.out ``` -------------------------------- ### Generate LightDock PBS Script for HPC Source: https://lightdock.org/tutorials/0.9.3/dna_docking Create a PBS script to submit a LightDock job to an HPC cluster. This script defines job name, queue, resources, and the LightDock execution command. ```bash #PBS -N LightDock-1AZP #PBS -q medium #PBS -l nodes=1:ppn=16 #PBS -S /bin/bash #PBS -d ./ #PBS -e ./lightdock.err #PBS -o ./lightdock.out lightdock3.py setup.json 100 -s dna -c 16 ``` -------------------------------- ### Visualize Receptor PDB with py3Dmol Source: https://lightdock.org/tutorials/0.9.3/membrane/data/tutorial.ipynb Loads and visualizes the receptor PDB file in a 3D viewer. Highlights membrane protein (MMB) with spheres. ```python import py3Dmol with open("3x29_receptor_membrane.pdb") as ifile: receptor = "".join([x for x in ifile]) view = py3Dmol.view(width=600, height=600) view.addModelsAsFrames(receptor) view.setStyle({'model': -1}, {"cartoon": {'color': 'spectrum'}}) view.setStyle({'resn':'MMB'}, {"sphere": {'color': 'orange'}}) view.zoomTo() view.show() ``` -------------------------------- ### Renumber Protein Atoms with PDB-Tools Source: https://lightdock.org/tutorials/0.9.3/rna_docking Renumber the atoms of the protein receptor partner using the PDB-Tools to ensure proper formatting for LightDock. ```bash pdb_reatom 1A1T_A_h.pdb > protein.pdb ``` -------------------------------- ### View Best Predicted Model in PyMOL Source: https://lightdock.org/tutorials/0.9.3/membrane Open the best predicted model from a swarm in PyMOL for visualization and analysis. ```bash pymol swarm_60/lightdock_115.pdb ``` -------------------------------- ### Extract Top Scoring Structures Source: https://lightdock.org/tutorials/0.9.3/rna_docking Use the 'get_top_structures.py' script to extract the top 10 scoring structures from the 'solutions.list' file. This creates a 'top_structures' directory with the best models. ```bash ./get_top_structures.py solutions.list ``` -------------------------------- ### Clean Failed Simulation Directory Source: https://lightdock.org/tutorials/0.9.3/faq Use this command to remove all generated files from a failed LightDock simulation to ensure a clean restart. This prevents issues caused by partially generated files. ```bash rm -rf lightdock_* init/ swarm_* setup.json *.npy top/ rank_by* solutions.list ``` -------------------------------- ### PBS Script for RNA Docking Post-processing Source: https://lightdock.org/tutorials/0.9.3/rna_docking A PBS script to automate the generation of conformations, clustering, and ranking of RNA docking predictions. It calculates the number of swarms and uses Ant-Thony to parallelize tasks. ```bash #PBS -N 1A1T-post #PBS -q medium #PBS -l nodes=1:ppn=8 #PBS -S /bin/bash #PBS -d ./ #PBS -e ./postprocessing.err #PBS -o ./postprocessing.out ### Calculate the number of swarms ### s=`ls -d ./swarm_* | wc -l` swarms=$((s-1)) ### Create files for Ant-Thony ### for i in $(seq 0 $swarms) do echo "cd swarm_${i}; lgd_generate_conformations.py ../protein.pdb ../rna.pdb gso_100.out 200 > /dev/null 2> /dev/null;" >> generate_lightdock.list; done for i in $(seq 0 $swarms) do echo "cd swarm_${i}; lgd_cluster_bsas.py gso_100.out > /dev/null 2> /dev/null;" >> cluster_lightdock.list; done ### Generate LightDock models ### ant_thony.py -c 8 generate_lightdock.list; ### Clustering BSAS (rmsd) within swarm ### ant_thony.py -c 8 cluster_lightdock.list; ### Generate ranking files ### lgd_rank.py $s 100; ``` -------------------------------- ### Submit RNA Docking Job to HPC Cluster Source: https://lightdock.org/tutorials/0.9.3/rna_docking Configure and submit an RNA docking simulation job to a High-Performance Computing (HPC) cluster using a PBS script. This script defines job parameters and execution commands. ```bash #PBS -N LightDock-1A1T #PBS -q medium #PBS -l nodes=1:ppn=16 #PBS -S /bin/bash #PBS -d ./ #PBS -e ./lightdock.err #PBS -o ./lightdock.out lightdock3.py setup.json 100 -s dna -c 16 ```