Autodock4 and Vina

Overview

Autodock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

The following versions are installed on the CSF:

• Autodock4 v4.2.5.1
• Autodock4-MP v4.2.2.1
• Autodock Vina v1.1.2

Autodock Vina is the new version and can run in parallel (unlike Autodock4). Autodock4-MP is a parallelized version of Autodock4 but should be considered experimental on the CSF. Users are encouraged to try Autodock Vina first.

Restrictions on use

Access to Autodock4 and Autodock Vina is not restricted. However users must abide by the license terms of the software and provide citations in publications.

Please see the Autodock4 license (GPL v2) and the Autodock Vina license (a permissive Apache license).

Set up procedure

To access Vina you must first load the modulefile:

module load apps/intel-12.0/autodock/vina-1.1.2

or, for serial autodock4:

module load apps/intel-12.0/autodock/4.2.5.1

For parallel autodock4 load one of the following modulefiles:

module load apps/intel-12.0/autodock/4.2.2.1-MP-omp              # Single node multithreaded
module load apps/intel-12.0/autodock/4.2.2.1-MP-mpi              # Single-node MPI
module load apps/intel-12.0/autodock/4.2.2.1-MP-mpi-ib           # Multi-node MPI

Any dependent modulefiles will be automatically loaded for you.

The 4.2.2.1-MP-omp modulefile provides a version that can be used on single Intel compute nodes (up to 24 cores). This also provides a serial version of Autodock4 MP which can be used to verify results from the parallel versions. It is highly recommended you do this to ensure the parallel versions are producing the results you expect!

The 4.2.2.1-MP-mpi modulefile provides a version that can be used on single compute node (up to 24 cores) using MPI.

The 4.2.2.1-MP-mpi-ib modulefile provides a version that can be used across multiple InfiniBand-connected Intel nodes and hence uses fast networking. The number of cores must be a multiple of 24 and the minimum number of cores is 48. This is the recommended MPI version.

Running the application

Please do not run Autodock on the login node. Jobs should be submitted to the compute nodes via batch.

Autodock4 Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

autodock4 -p macro.dpf

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Autodock Vina Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

# NSLOTS will be set to 1, use it to inform vina how many CPUs we requested
vina --cpu $NSLOTS --receptor file1 --flex file2 --ligand file3 -out outfile

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Autodock Vina Parallel batch job submission

Note: Autodock4 will not run in parallel (see Autodock MP below).

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings
#$ -pe smp.pe 8     # Number of cores (2-24 permitted)

# NSLOTS will be set to 8 (in this case), use it to inform vina how many CPUs we requested
vina --cpu $NSLOTS --receptor file1 --flex file2 --ligand file3 -out outfile

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Autodock4 MP Serial batch job submission

We recommend running the Autodock4 MP version’s serial compilation to give you a set of result against which you can compare the parallel version (see below for how to run in parallel). Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

autodock4_serial -p macro.dpf

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

To see the complete list of command-line flags simply run autodock4_serial on the login node without any input file.

Autodock4 MP Parallel batch job submission (multithreaded)

Note that the OpenMP (multithreaded) version uses the same command-line flags as the above serial version with the addition of a -r option for the seed type (if unspecified the default_seed is used):

-r seed_type

The seed_type accepted values are:

• same_seed – Use a hard-coded seed value, useful only in doing performance measurements by deterministically running the docking.
• default_seed – Use the time of day plus the threadid for the seed.

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings
#$ -pe smp.pe 8     # Number of cores (max 24) in a single node

# You MUST set this to inform autodock how many cores to use:
export OMP_NUM_THREADS=$NSLOTS

autodock4_omp -p macro.dpf -l macro.dlg        # Send output to logfile macro.dlg

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Autodock4 MP Parallel batch job submission (multi-node)

Note that the MPI version (multi-node) uses a different set of command-line flags to the above two examples. It requires the following options in the order given here:

docking_list_file docking_base_directory status_directory seed_type map_file_usage

where

• docking_list_file: file containing the list of ligands to be docked
• docking_base_directory: base directory containing the ligand directories created with the python scripts for the virtual screening setup (eg. the ‘Dockings’ directory from the UsingAutoDock4forVirtualScreening_v4.pdf tutorial)
• status_directory: directory containing the following status and performance logging files, updated in real time as each docking finishes
• seed_type: Indicator for the value used to seed the RNG, values must be:
  • same_seed – Use a hard-coded seed value, useful only in doing performance measurements.
  • default_seed– Use the time of day plus the threadid for the seed.
  • unique_node_seed– Use the time of day plus the threadid plus the MPI rank for the seed.

  Note that in this version the MPI ranks are single-threaded.

• map_file_usage: Indicator for whether or not grid maps should persist in memory on the slave nodes from docking to docking – value must be either reuse_maps or reload_maps.

Refer to the paper Multilevel Parallelization of AutoDock 4.2 for further information for these runtime options and for details on the parallelization strategy and performance improvements.

Further Advice on Running MPI Jobs

We have received the following advice from a CSF user who has tested autodock4_mpi:

Assuming you are running the job from the scratch directory, the following files should be placed there:

• receptor.pdbqt – to be read by autogrid4.py, a script that can be downloaded from the AutoDock website. It must be run before the autodock4_mpi job to have the grid map files previously generated (see below).
• file.gpf – file you use to create the grid map files. Take into account that if you reload the grid maps, all the gpf files used must be also in that directory.
• ligand_receptor.dpf – a file you create with the prepare_dpf4.py script that is available on the CSF by doing:

  module load apps/binapps/mgltools/1.5.6
  $ADTUTILS/prepare_dpf4.py -l ligand.pdbqt -r receptor.pdbqt
  

  This will output a ligand_receptor.dpf file by default.

To run the autogrid4 command to generate grid map files run:

module load apps/intel-12.0/autodock/4.2.5.1
autogrid4 -p sample.gpf -l sample.glg
  #
  # This will also read the receptor.pdbqt file

For further information see the tutorial on the AutoDock website.
You will also need to create the following directories using the mkdir command in your scratch area (we assume you are running from your scratch area):

• etc/ (here one must save a docking.list file with a list of all the names of the ligands. The UsingAutoDock4forVirtualScreening_v4.pdf tutorial can help to know how to create it)
• results/pdbqt_lip_rules/ (inside the pdbqt_lip_rules/ directory one must save all the ligands.pdbqt files)

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd                   # Job will run from the current directory
#$ -V                     # Job will inherit current environment settings
#$ -pe orte-24-ib.pe 48   # Run on faster IB-connected h/w (multiple of 24 cores)

# $NSLOTS is automatically set to the number of cores given above
mpirun -np $NSLOTS autodock4_mpi docking_list_file docking_base_directory \
                                     status_directory seed_type map_file_usage

where the path of the docking_base_directory and the status_directory should be the directory where all the files have been saved (scratch in our example).

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Once autodock4 has run, it will generate:

• The glg file or files (depending on the number of file.gpf used)
• The dlg files
• The following files: docking_performance.csv, failed_dockings, submitted_dockings, successful_dockings.

Further info

• Autodock4 website
• Autodock4-MP website
• Autodock Vina website

Updates

None.